I hateeeeee the two timeline thing so much, both because it (1) was introduced as a terrible fan theory with absolutely no evidence, in the classic “what if this happens…” sense, and (2) because I think it is absolutely awful writing, but I cannot agree with you that it was debunked. This episode all but confirmed it for me.
To wit: (1) Dolores’ “WHEN ARE WE” freak out is every bit as on the nose as Bernard’s “What door?” last week. This is the Westworld style, and I do not believe that was an accident.
(2) How the fuck else to you reconcile using the same actress for William’s onboarding host and MIB’s “Oh… it’s you”? If that’s an accident, this show is even more poorly done than I thought possible. But seeing as the writing on this show has been clunky and hackneyed yet the production, direction, and exposition has been nothing short of brilliant (which is why everyone is still watching it), I’m a million times more inclined to think it’s just bad expository scripting (and that yes, this is two timelines) and not incompetent casting/directing, since we’ve had largely excellent casting and directing so far.