They say PF2 isn't based on 5e, but the description of their new game concepts screams otherwise. They have a unified proficiency system that replaces BAB, save bonuses, and skill ranks, just like 5e's proficiency bonus. They also have a new character building paradigm (race/background/class) similar to 5e. They even take a cue from 5e's recent evolution and incorporate the idea of race, background, and skill feats.
To me, it seems like the "this isn't 5e the way Pathfinder was 3e" is more a way to preserve their own individual identity than an accurate description of the new game system.