So I know everyone here has already watched this through but my thoughts - I'm about to start S01E09.
I think the two timelines do exist. What convinced me was when MIB saw the one lady out in the open (Same lady as who welcomed William) and made the comment "Ford keeps you guys around, etc."
I'm betting on William really sinking into this world, his real life fiance/wife dying, and now he's the MIB. Per earlier episode, two other guests tried talking to MIB saying "We really love your organization" -- I think William started some sort of charity after his wife passes away and sinks further into the Westworld.
My leading theory anyway. I definitely think we have two timelines.
PS: Best part of this show is the subtle phrases, clues, etc. "What door" was one of my favorites.
PSS: I hope Elise comes backs, loved her character.