For Miqote and Viera there are no lore issues. The player character isn't the world, but a special individual. If players had to follow the lore, then only a single person on the data center could ever be Whm at any given time. We are supposed to ignore lore for such things.
As for Seraph, the encyclopedia implies that she is the true form of Lily. That the Scholar summons the fairy, and when she spreads her wings everyone is suddenly consoled (looking at you Consolation). And for a pact with Feo Ul, there's no lore reason that we shouldn't be able to. Especially considering that we technically haven't made a pact with a fairy ourselves, but are using someone else's