It's not a reboot.
It's essentially continuing from before but with certain elements carried over from Doom's Battleworld, thanks to the Molecule Man, and potentially certain things changed.
The world thinks Reed, Sue and the FF (Future Federation) are dead, but they're essentially now semi-cosmic deities who are using Franklin's powers combined with Reed's new powers (that were Doom's, that were the Beyonders + Molecule Man's) to recreate all the universes that were lost in the Incursions.
They started recreating our universe first, so what was the 616 is now the Prime Universe, and certain details may be incorrect and certain things won't have happened as it's based on Reed's knowledge and Franklin's imagination.
It's similar to Heroes Reborn, or when AF were alive again after Chaos War, really.