I must ask, though...
Are there any levels that are different enough that would work in one but not the other (don't forget the modded triggers in GenesisGroundX) as long as they were small enough?
The obvious Genesis solution for Tricky 30 ("Don't Follow Me") doesn't exactly work in DOS Lemmings as-is, I think because of subtle differences in fall distance calculations for miners. In DOS Lemmings the level is still solvable but requires some RR manipulation, which in turn (if I recall correctly, it's been a while) is too big an RR change to do in the actual Genesis game (remember that you can't change RR while paused in Genesis).
It's also well known that some challenge solutions only works in one version and not the other. For example, the best solution for Tricky 23 loses 2 lemmings on the Genesis, rather than 1 as in DOS, and the 2- or 3-digger solution for all the "We All Fall Down" levels doesn't work in DOS.
I forgot whether the one-way miner bug (you can't mine one-way-walls in one of the directions, forgot which) in DOS Lemmings is present in Genesis or not. If it's absent in Genesis, then playing it on Genesis would allow more levels to work.
Like Amiga lemmings, the clock on Genesis lemmings runs out a bit faster than it does in DOS, which would affect the difficulty of levels like "Just a Minute (Part 2)" for example.
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But yes, for most levels it probably won't matter, especially if you just care merely about solvability. But that's the difference between 90% (random number) compatability as opposed to 100%.