I think this might be the reason that people run the game on SNES

In short, Sega players die when attempting to finish a level with this trick, while SNES players go onto the next level as normal

I believe for that trick to work you have to touch the right side of the screen, then move back left before hitting the goal. That's how it works on SNES at least.

SNES and Genesis were kept separate due to different loading times, but aside from that I wouldn't be surprised if there are other version differences too. I think it's more of a coincidence that folks up to this point have ran on SNES than anything, since there are so few runners.