it has nothing to do with the media, Snes and Super Famicom have the same media but are seperated out. Tg16 and PCE have the same media, PCECD and TGCD have the same media, hell even the genesis and 32X have the same media i.e. cartridges etc. The reason why they are split is because they all have HUGE libraries of game (in the 100's) that were not localised for the west so to some its almost like a seperate system entirely.
Most of the Sega Cd library are NOT ports of Genesis games, the Streets of rage you just posted was a Sega Classics COMPLIATION disc of genesis games, they are not supposed to be updated or different from the genesis originals.
It didn't matter what media a dos game came on, it woud still work on Dos. However a Sega CD game requires a Sega CD, a genesis will not run the game.
Ports of the same game on different systems is irrelevant anyway as most third party games end up on multiple systems. What would you suggest? Merging the snes and genesis since they share a few hundred games?