Sure, it has puzzle and backroute-proofing potential, but it ultimately means more things to mentally keep track of in-game (particularly if multiple workers have been assigned multiple different permanent skills - yuck! ) and is therefore potentially annoying.
At first I wasn't sure what you meant here, but after a bit of thought: if multiple workers have been assigned different permanent skills, and remover objects can remove those skills individually, then yes, you have to mentally keep track of which permanent skills are still on each lemming, and this could be annoying.
However, if the only form of permanent skill remover is one that removes
all permanent skills, then there is an immediate visual difference, and indeed one less thing to keep track of, since the lemming is simply normal again.
As for the other considerations: the main distinction is that if the remover is single-use
or one-lemming-at-a-time, you can bring a particular permanent skill past it, by first "feeding" it another permanent-skilled lemming. If it affects all lemmings, you absolutely cannot bring a permanent skill past it except by bypassing it (e.g. building over the trigger area).
Both ways have puzzle potential; but I suspect that puzzles will be more interesting, and cleaner, if the remover is absolute. Then if you need, for example, a floater on the other side, you have to find some way to either bypass the remover, or find a way around it, or do without the floater on the near side so that you can assign it once the lemming is already past the remover; and having these different possibilities already creates an interesting space for both the designer and the player to explore.