I think the first thing to remember is GW HAS never been one to shy away from ret-conning their fluff, if they want Nagash they will ret con as appropriate.
On the other hand, if they're advancing the story, then no ret-conning is required, instead it's what we (speaking as someone who used to write plot for a LARP system) call Flange, where you write a story to enable a specific character or event or item that might otherwise not really seem feasible (I think pros tend to call it Deus Ex Machina, but chumps like me call it flange). However, as the most powerful Liche ever to have lived (existed?), it is entirely possible that it doesn't really matter whether the Tomb Kings like him or not, the thing with Unliving beings is they're always susceptible to being controlled by the most powerful Necromancers. So if they don't like him, they can sit there and seethe and rage all they like, but if Nagash is pulling their strings, they're still going to have to do his bidding. A bit of internal struggle within a single faction is always good fun.