The alternate reality theory is just too much, even for X-Files. It has no basis after 10 seasons, but they keep stoking that fire with little comments here and there that contradict S10's finale - or at the very least put into question what S10's finale was.
I have to believe Jackson is William, and is just learning how to use his powers like the alien Bounty Hunter and Jeremiah Smith.
They'll start to connect dots to have stuff make sense, but then make comments that add to the alternate reality concept. It's so aggravating.
Scully's moment with Jackson/William was pretty poetic though and tied up the sentiments behind season 8 and 9 very well. I think at this point if they're going where I think they're going, they need to bring back Billy Miles is some capacity to drive home the point that this is who William is supposed to be character wise.
Finally, we need more from Skinner's half turn half non-turn. Right now its just kinda there to provide a way to have CSM back but feels a little hollow or forced, I can't decide which.