Dazed and confused.
It's just a matter of scale. For North Pole warp portal see Eye of Terror. If there was a huge assault from and expansion of the Eye, it would mean a series of unlikely alliances between all the humanoid races to try and combat it. Sure, the Nids would still be chomping their way towards Terra, but if the 13th black crusade was only a precursor to something much, much bigger, like a demon primarch(s) led incursion, they could be temporarily ignored. It would be very easy to scale the whole thing up to a suitable level.The problem here is that there are three possible endings to 40k: Chaos wins, Tyranids consume the galaxy, Necrons seal the warp and win. Fantasy really only had one outcome, chaos winning; the warhammer world had an open wound to the realm of chaos in the northern pole (with no way to close it.) And it was only a matter of time before the inhabitants of the warhammer world lost enough ground to chaos, the events of the End Times simply hastened that outcome.