"Bubbling under the surface" doesn't make it the main plot of BfA. That's the point.
Yes, all of those topics always were there and it's good that they were there. The problem is the faction war storyline was all over the place and further fueled by EVERYTHING Blizzard released as promo/advertising/marketing material surrounding BfA. And then to say "that's it", wrap it up in a tiny patch with a tiny questline feels just... wrong. It feels like they abandoned the idea and just wanted it to end so they can move on from it because not only the players but the devs themselves are sick and tired of the faction war topic they started.