I thought the Genesis/SNES thing was hearsay that was disproven on this very forum a few months back? They both played pretty much the same, and were pretty solid ports for the pre DC era - captured the spirit and the feel of the game, but wasn’t quite there. In this case mainly smaller sprites, shittier sound, and lots o’ missing frames.
Nevertheless your point pretty much summarizes the entire lost art of arcade ports. Porting an old game to a newer system tends to be more of an effort of effectively copying the visuals, the gameplay, the glitches, etc. as best as you can. Older consoles were more of getting the feel and the gameplay down more than anything. Maybe you weren’t going to mistake PC-Engine or NES Gradius for the arcade version, but you could tell it was definitely Gradius.
In the case of fighting games, you’re dealing with different arcade hardware architecture, console limitations vs. arcade power, etc. so things do get lost. In the case of Neo Geo fighters, SNK had to reprogram their ports from the ground up since reportedly the Neo was using Assembly language which pretty much nothing had to by the mid-90s. Effectively, they had to rebuild the game all over again. With that in mind, is it particularly surprising that they’d have notable differences? Same story goes for Capcom’s fighters to a slightly lesser extent, but it still didn’t stop them from putting out inferior ports of, say, Alpha 3 for years.