I don't know if it's possible to get an exact answer about this. All I think can be said for sure is that after a while the story team settled on a Matoran number of one thousand(ish), but a lot of the media doesn't reflect this, probably because whoever was making it just didn't have that number in mind. The very early online stuff often shows very few Matoran then the movies show vast crowds.
While I do remember the 'twelve Matoran in each village' idea, I don't know if it was decided from the start, and I think Greg soon stated they were dropping it due to the Kohlii match in the first film showing a lot more than just twelve. The second MNOLG might have been made with it in mind, given that there seem to be fewer Matoran than were shown even in the original MNOLG.