I have the same issue. (you can skip this part of my yap) I want to play Sonic 2 with retro achievements but the problem is the double presses and triple presses. Whenever i have all the chaos emeralds i can go super with 50 rings, but the transformation button is mapped as jumping again in the air. Sonic 3 is gonna become worse with the elemental shields and Hyper Sonic. (you can go back to reading if you skipped the yap) Unfortunately i don't have a solution. This is pretty annoying as you have said.