I had an idea for the games that are both for the Sega CD and 32x. I think you should combine them, just like with the Fahrenheit cover. It's just an idea, though, and you don't have to do it, but I just thought i'd throw it out there and see what you guys think of it.
I had the same idea a couple of weeks back.. I actually have already made a dual cover for Supreme Warrior.. but I have not uploaded anything yet.

Combining the two covers just makes sense if the game was released that way.... Otherwise it would be pointless?
I was thinking about what your said...
How can this be different from all those Wii covers for Gamecube games
True that it is a single game and not design to replace 2 other cases, but it was certainly not released this way.. Nor hundreds of other games with covers on this site.
I mean, At least the cover I made displays the systems it was originally intended to be used on.

My 2 cents