Which emulators are legal for use on this game? Are all official releases of Comix Zone allowed, like the Wii Virtual Console?

I don't see why not. Additionally, you've ran the Steam version, my run was done on the Sega Smash Pack 2 - another PC version (both runs were approved on the leaderboards), and mecharichter used the Xbox360 version in his SGDQ 2013 run (which was approved by SDA).

From what Wikipedia lists, the Gamecube, WiiVC, PS2, PS3, PSN, PSP, Xbox, Xbox360, PC, iOS, and Android versions all appear to be direct ports of the game with no discernible differences, and are also probably safe to add as acceptable platforms on the leaderboards.

I know the GBA port has a fair bit of mechanics differences, and I think we can at least wait on adding that as an available platform for that reason.

If a mod can respond to this thread with their thoughts, that would be great.