I'm not sure I follow all that. All I can say is that if that is the final episode, it isn't as satisfying as the previous few "final" episodes of
The X Files. It did, however, kill off a lot of major and recurring characters and agents. I can't remember so may characters dying in one episode since
Torchwood or
Blake's Seven. One person who looked to be dead, didn't really die, however, which leaves the story open to continue, and that was exactly what he wanted - for everyone to think he is dead.
Mulder isn't wearing the glasses. Scully isn't talking about the marriage and episode is disconnected from the past. But, even then, the final is good one. The story flows nicely and there is no moments where you'd like to push fast forward.
I agree with you, that it seemed incongruous to insert all those 'monster-of-the-week' episodes book-ended with the 'William' story. Also, Mulder may have forgotten his glasses, but surely that was a major reveal at the end about Scully which will certainly affect their ongoing relationship? I also found that the flashback nature of this episode hardly made it "flow nicely." I assumed some of what we saw was not in real time, but were William's premonitions of the future, but I was unable to tell what was real, and when it was the real Mulder or the William impersonation of Mulder. Consequently, I thought it was hard work to follow.