well, my good feller, for illegal voter registration that isn't discovered until after the 90 day window begins, a vote cast by such voter does not become legitimate, no. but my guess is that this happens so infrequently that the effective solution is to jail the fraudster. there would be little value in "subtracting" the vote from the certified count simply because the documented number of such cases is so very small compared to the total count.
this is part of the reason why most people oppose special IDs or almost any method aimed at reducing fraud. they are trying to combat a problem that is so very minor that even if they succeeded completely and perfectly, the net result would be practically meaningless. the other part that i mentioned elsewhere in this thread is that purging rolls within the 90 day window risks the possibility of removing legitimate voters from the rolls by mistake. lawmakers decided that avoiding that possibilitiy was more important than a small number of fraud votes slipping thru. bear in mind, too, that some fraud votes will cancel each other out becuase, beleive it or not, both sides have been known to do it.
now the FEMA aid for ID thing doesn't seem incongruous to me, no, because any state-issued ID would be good enough for that. the voter ID that Dems oppose, as i understand it, is a special ID issued by the state specifically for the purpose of voting. the process of issuing such IDs could be regulated to the advantage of one party or another, depending on how it's carried out. since neither side is in a trusting mood these days, issuing such IDs is naturally going to be opposed.