Fabian brought up some points yesterday that made me wonder which side of this issue I would be on. In general, I don't think having more than one version of a game is bad, nor do I think that changing versions is bad either, as long as it's significantly explained. The reasons for multiple versions can range from differences in graphics and sound (Super Mario All-Stars), to new levels (Prince of Persia SNES), to version-exclusive glitches (Flashback Genesis).
But this is a special case that I don't think will work. SNES Doom tries to be PC Doom and fails hard. The whole time I would watch a TAS of it, I'd be thinking "I sure do wish this was a TAS of the PC game." As I understand it, there's no new content on the SNES version. The graphics are different, sure - I think we have 12 frames a second on the SNES. There may be new glitches in the SNES version, but unless they are significant, they aren't going to make this run entertaining.
A similar example is the
Sonic Genesis remake for GBA. I really doubt the glitchy physics are going to make this lag-filled game entertaining, especially with the great original Sonic 1 in our memory.
So I guess what will happen is that someone will eventually TAS one of these types of games, and we'll have to see what kind of response it gets. If the version is truly unique enough, then it will get the praise it needs to get published. I HIGHLY doubt this will happen with SNES Doom.