Clearly the incursions did happen. There's been far too many references to them in various All New, All Different books to conclude it didn't. The general public even know of them happening this Time Runs Out and Secret Wars #1 still likely occurred.
I'd take Wakanda being restored as it was in New Avengers #1 as everything else that's been reworked by Secret Wars. Old Man Logan, The Maker etc all land in 616 and so on, I don't think this is any different. It was mentioned early in Secret Wars a portion of Wakanda survived on Battle World and we saw T'Challa react to that. I'm guessing the Wakanda we see here is that one, one that never went through all the incursion stuff and has landed in the new regular Marvel Universe.