By "they" did Greg mean the Toa Nuva? Not the Cube & Symbols I presume? 
Yes, I'm pretty sure he meant the Nuva themselves. I mean, Artakha made the Symbols/Cube first-hand, so he knows they can exist. 
I suppose a better way to put it would be that Artakha knew the Symbols/Cube had the potential to be relevant.
That's a good point, but then what if, say, the Nuva had awoken Mata Nui but not realized they were supposed to free the Bahrag, and Mata Nui says "Me face be dirty yo yo!" and they head off to free them, but one of them dies on the way? Would it not be wise for it to be possible to find another Toa of the same element?
Of course, now there's the Red Star for such things... or there was... and the Bahrag weren't supposed to need caged, but yeah.
Besides, the difficulty for Roodaka was in painfully cutting out a piece of the cage and encouraging the Toa to shoot at her. Once she did that, does it really matter which Toa she gets to shoot at her? She's unlikely to coerce any Toa into willingly freeing Makuta, so this same basic strategy I think would be needed anyways, and likely she would want to use the Visorak so she's not going up against Toa by herself... so why not use this attack on the same six Toa, who have a clear motive for opposing her personally? They didn't know attacking her would free Makuta.
So I don't think that would be a major problem for canon consistency. And if it had to be the same Toa, why would it not be simply stated as such?
I imagine Mata Nui would have had some trouble awakening, then, if the island hadn't been cleared (though as you said, that was supposed to happen on-schedule and the only reason the Bahrag ended up caged in the first place is because Teridax woke them up prematurely, so when you think about it, the Bahrag Seal wasn't even supposed to exist and the Toa Mata probably would have transformed via some other method), even though on a tangential note, I really don't see how breaking through the island would be any sort of obstacle for Mata Nui, cleansed or otherwise...I mean, he's gigantic...but I forgive that bit because of Bionicle physics. 
Anyway, I suppose you're right about Roodaka. Although thinking back on it, now I'm not even sure how I feel about the "evolving" Toa Seal bit.
But that was basically a seventh element, or maybe a non-elemental use of electricity, added beyond the six that actually made the protocage. I think the substance of the cage is not determined by the elements that are used to make it; the Inika thing is just like if something touches a live wire it will get a charge in it; the thing in this case happens to be a cage they just made.
But again this need not affect your theory, just analyzing as I go. 
I believe it was non-elemental but you have a point. I may go back and revise some bits and pieces of this idea, because now that I think about it, I'm not sure there's enough to back up the "evolving Seal" part. It's actually the more presumptuous part of this theory.
So my guess is that where this is headed is that the Cube translates Nuva power into a merged Mata beam? *reads on*
No, but that is a good alternative to this theory. 
Where is the bit about the materials from? I didn't see it on the Mata page on BS01. Couldn't that just refer to protodermis? They provided the entire protodermis of the whole MU/giant robot.
I'm not sure where I read it, I just know that it's been ingrained in my head for a while. I'll try and find the source. Protodermis probably made up a large quantity of the "materials," but I assume that the Toa Mata's spirits and whatever it is the people in the MU use to imbue something with Elemental Power and also Toa Power were provided as well.
However, I think everything else in this part makes sense. I might add my cyberclay theory would make explaining that easy; Artakha could read the equivalent of DNA in the coding of the protodermis particles. Or, a non-cyber, molecular system in protodermis may explain it, or something in their brains, or something in Mata Nui's brain, etc. all of which it's possible Artakha could gain access to, or be given it.
Cyberclay theory? I'm unfamiliar; I'll have to look into that. 
Or, he may simply extrapolate from what happened if he experimented by dipping various things in Energized Protodermis, and found that dipping masks in producing Kanohi Nuva, and understood their physics and requirement of Toa Nuva. 
I suppose he could do that, although he does have the Mask of Creation which can save a lot of time that would otherwise be spent on trial and error.
Just to be clear, I agree this is plausible -- not because the actual elements involved matter IMO (so if one was a Toa of Iron, it wouldn't make a difference in the actual substance), but a universal difference -- like being a Nuva or an Inika -- may still matter.
I considered something similar to that at first, but I couldn't really think of a way to rationalize the idea that all of the Mata, all of the Hagah, all of the Inika and so on are inherently different from one another as well as other Toa. Though I guess I could have simply suggested that certain Toa are programmed to be a part of a certain team, while others are programmed to be solo, OR I could have theorized that Toa Power is different between each Toa; however, each of the Metru's Toa Power came from Lhikan, the Inika's from the Red Star(?), the Mata's (presumably) from Artakha and so on, thus explaining why one Seal would depend on which Team they were from. Yeah, definitely gonna do a 2.0 of this theory when I have more time on my hands.
Ah, I see, you're not going where I thought you were. This is actually the running theory I have had and have posted. I thought where you were headed was that the nature of the Toa only when they made it matters, so it would be a Mata Seal, and they are Toa Nuva, so the cube would translate their Nuva power to a Mata beam.
As I said, that's a great alternative, though I'm not surprised I didn't think of it. 
So, you're not necessarily saying this happened, but that Artakha wasn't sure if it would happen? Also I'm still confused because I thought you were saying the Seal transformed when they did, so it's not just a Mata Seal but a Nuva Seal. Here you say Mata Seal... Hm...
Sorry for the confusion, I was worried that my throwing around terms like "Mata Seal" and "Nuva Seal" would get a little crisscrossed.
At the time I was saying that the Mata Seal had, in fact, evolved into a Nuva Seal, but after re-reading my theory I realize that this particular tenet is unnecessary--the only things that are integral to this theory are the ideas that the specific Toa who create a Seal are the only ones that can break it, that a Toa's Elemental powers can only be a part of one Seal at a time, and that the Nuva Cube is intended as a contingency device to be used should one or more of the Nuva be unable to contribute to the creation/destruction of a Seal.
So are you proposing that one group of six Toa can only have one existing protocage at a time? If they trap the Bahrag, and then go out and need to trap some other villain, the second trap would fail?
Eh... I don't see why it would be a problem for there to be however many protocages they need to make. The one the freeing beam is shot at -- and the one the Nuva cube is in front of -- is the one that is freed.
This was more or less intended to resolve a hypothetical scenario, that being "what happens if the Toa Nuva have two active Toa Seals and then someone places the Symbols onto the Cube; does only one Seal break or do both?" Personally, I like the idea of a One Seal Limit because I think of it like this:
1) Artakha creates the Symbols in order to serve as storage space for the Nuva's enhanced Elemental Powers should the turn into Toa Nuva.
2) Knowing that Toa also have the ability to create a Toa Seal, Artakha creates one Nuva Cube that will correspond to whatever Nuva-created Seal is active at a given moment (assuming that there can only be one Seal at a time).
3) When Artakha senses that the Toa Mata have transformed into the Toa Nuva, he teleports the Symbols and the Cube to the Nuva's location (or, alternatively, he keyed the Symbols/Cube in to the Mata's Elemental Powers and gave the objects the ability to detect when the Toa had transformed, which would mean that the objects had become relevant. One could even suggest that since the Toa Nuva may not have been destined to transform in conjunction with their creation of a Toa Seal, then the Cube wouldn't have teleported along with the Symbols in such a scenario because it wasn't relevant yet. But that's another theory for another day, I guess.
)
Now despite all my quibbling, I think this part of your theory is a brilliant point, and enough that it deserves some recognition. 
However, I think you've got the reason for the failsafe backwards -- I don't think anything that happens to the Toa who makes the Seal after it's made affects it; I think the cage remained a Mata Seal, and Artakha wasn't certain that Nuva would be able to unlock a Mata Seal.
Or to put it into non-personal terms, since I'm pretty sure any Toa of the same element would suffice, I think the cage remained a Toa Seal (did not become a Toa Nuva Seal). So the cube would translate the Toa Nuva power to Toa power, just in case it wouldn't work. However, it did work, and proved unnecessary -- but the Kal took advantage of it anyways.
Thank you, although now I kinda like your idea better anyways. However, I suppose that the two failsafe ideas aren't mutually-exclusive; Artakha may very well have built the Cube just in case the Nuva's power wouldn't work AND just in case one of them happened to be missing.
If you're right that Seals can change types if the Toa who made them change types, then this could provide another reason for Roodaka to need the Hordika's power. When they were turned to Hordika, the Toa Seal could turn into a Toa Hordika Seal. This would help explain her actions if I'm right that a different Toa of the same element could be used to unlock it. Or, I guess, you're theorizing that Artakha may have believed it so, even though it wasn't so, therefore likewise maybe Roodaka believed the Seal might change as the Hordika changed. I dunno.
That would help explain it, but I think I've pretty thoroughly abandoned the "evolving Seal" idea by now. Oh well. 
Anywho, your core theory, even the main part I disagree with (that the Seal changed when they became Nuva) is very plausible and well-thought-out and suchnot, so here is that recognition. 
Wow, awesome! Now I can have unlimited access to Nongu, whatever that means.