I think it is a question of different brands or models of floor flanges. Specifically, how thick it is.
Yes, the flange sits on the floor, and the commode sits on the same floor. So if the two are compatible, the seal will fit.
But let's say, for the sake of illustration, that the maker of the commode is in Vermont, and in Vermont it has been customary since the beginning of indoor plumbing that floor flanges are half inch thick. (This is hypothetical.) Having never seen anything else, the commode manufacturer build his commodes to fit a half inch flange. Then, a customer in Arizona buys one of these commodes, and in Arizona it has been customary since the beginning of indoor plumbing that floor flanges are quarter inch thick. (Again, hypothetical.) In this case, the customer in Arizona would need to shim his "Arizona-flange" a quarter inch up in order to fit the "Vermont-commode". That make sense? Last time I walked thru my local hardware store, I think I saw at least half a dozen different floor flanges on the shelf, so odds are there are a couple of different thicknesses out there.
Just a theory.