I think you've put more thought into this than the writers of any game in the franchise have. Don't over-think it. Gameplay concepts such as the number of chaos emeralds or super emeralds for each characters super forms, or even how many there are... Things like that are decided before a story is put into place, especially in the 2D games. If Tails and Knuckles get super forms in episode 2, it will be from the seven regular old chaos emeralds, with no extra explaination given.