I doubt the Okudas had any clue what Discovery would be about when they wrote that entry. I think they were just making the same assumption that the IDW comics' writer Mark Johnson made -- that the discrepancies in the first two movies (like the oddly gigantic starships and overbuilt Earth cities, or the presence of a "Delta Vega" planet that's evidently in Vulcan's star system or nearby) were evidence of earlier timeline differences -- and came up with a way to reconcile that with the filmmakers' model that the changes were caused by Nero's arrival. If they were thinking of "future-proofing," it was probably with an eye toward whatever other changes later movies might introduce.
(As I've said before, the irony is that Beyond is easier to reconcile with Prime history than the previous two movies were.)
