What if... something about using his powers makes him go bald as a side effect, like great exertion or prolonged use. It could have been the latter in the original timeline, but the former in X:A .
So, for a hypothetical.... Maybe in the first act, he's trying to wrestle the Horsemen back to the good side and right after, when he's tired, out of breath and his head hurts... he runs his hand through his hair and a tuft of hair comes out (not leaving a bald spot or anything, but enough to know what's going on)
The, during the big act three climax where Xavier has to push himself harder than even
he thought he could to stop Apocalypse, all his hair comes out during.
I think something like that could work. It's a reasoning that works for Xavier in either timeline, but not dependant on Apocalypse having been faced in both. Just Xavier exerting himself (or again, it just happens after prolonged use of his powers... but the exertion Apocalypse puts him under makes it all happen at once).
Or we're thinking too hard about this.

But I think something like that would fit.