My theory is that the Rahkshi were not purposely created by Makuta, but when he legged it he sheltered somewhere and got really angry, and accidentally projected some of his power into six of his remaining Rahi, and they morphed and mutated into the Rahkshi. What do you think?

Well, it's a good theory, were it not for the fact we know exactly how the Rahkshi were created.

Basically, Makuta has been creating Kraata for ages.
Seems that six Kraata (possibly in the rare seventh evolution form) encountered Protodermis, and became Rahkshi.

Not entirely sure whey they now carry Kraata around with them, aside from the whole "gain strength when the Kraata evolve" thing.
Must be mutually beneficial, since the Kraata are now protected inside the Rahkshi as they evolve, and the Rahkshi somehow draw power from them.

A truly symbiotic relationship.

Well, it would've been a good theory a few months ago.. but now we know exactly how they were created. Makuta made the Kraata, then the Kraata evolved into the Rahkshi via Protodermis. BTW, Post in the Official Rahkshi Topic next time, K?

FH