Multiple Timelines Not Likely
A big theory going around is that William and the Man in Black are on separate time timelines. The biggest evidence against this from my vantage point is when Luke Hemsworth's character metions that Dolores is out of her loop and they send someone in to grab her. He also comments on The Man in Black, that he is a VIP and can do whatever he wants. In the Stray he goes with Elsie to get the wandering Host. They could be playing with our eyes on this, but it establishes that they are happening within a similar time period, but Hemsworth's character is for sure part of a current timeline thus tying all the characters together. This is not to say that the show isn't using time jumps, a la Game of Thrones, but they seem to have explained that things are happening within the same timeline and we the fans are breathing life into a theory that isn't really there. Would be interested in others thoughts on this. I am by no means an expert on the show just a fan who has really enjoyed the discussions for this show.

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It's just that to even put forth the theory that we are seeing an extended flashback you have to call it something other than a flashback. Because there are obvious flashbacks already in the show.
Two loops would probably be a better term, because according to the theory we are actually seeing two different loops with Delores one with and one without William.
The issues with the two loop theories are many, but that will never stop the tinfoil. I've read through many Darrio=Benjen=Euron diatribes in my time and this is nothing compared to what the GoT crowd dreams up in the GRRM writing gap.
I happen to not thing the two loop theory to be very interesting. Especially since it clearly can't show the event that killed Arnold because we have had Logan specifically mention it.
So at best William=MIB and we get the origin of why William turned black hat. But why would we really need a season long hidden flashback arc to show us that?
And if that's true it means William/Delores don't find any answers to why she is becoming sentient because William/MIB gets stopped before finding any clues and Delores gets reset. So the inevitable end to that would be a "holy shit this was all a big flashback that went nowhere because the loop got reset".
I think my biggest issue with the theory is two parts:
1. We know the hosts are often rebuilt as new narratives are created. Are we to believe that Dolores has been on the exact same loop as the rancher's daughter dropping the same can of condensed milk for the last 30+ years? That doesn't seem likely to me.
2. Dolores is experiencing flashbacks while she is with William and Logan that I assume are from a previous build. I believe that like Maeve (who we know is a "present day" character) these flash backs were triggered by the "reveries" added in the update we see in the first episode.
I know there is some evidence for the theory (and after I heard about it and re-watched the first 4 episodes I bought into it too), but I feel like there are some gapping holes that don't quite make it work for me.
However, I'm coming around to the two timelines theory because of the evidence and coincidences that seem to be stacking up.
Before, I felt that the storytelling was intentionally straightforward. That is, characters say certain things serving as segues into following scenes. Now I'm entertaining the thought that the dialog is intentionally being used to deceive the audience. That is, it's being used to make the audience believe they are the same timeline when they are not.
So, in this case, Dolores is clearly out of her loop. Her visions imply that she's been out of the loops before.
I could possibly be wrong and would gladly see hard evidence to put this speculation to rest.
William has been shown in both places though. When Dolores was in Las Mudas, the guy who tried to take her back to her ranch was stopped by William ("She's with me.")
I read another good point elsewhere too. If William is the MIB, why does the MIB feel clueless about the maze? Wouldn't he know exactly where to go? He wouldn't have to bother with Lawrence and Armistice. He could go directly to Pariah (unless the maze is known to change).
What's funny, is the facial expression of this guy while drawing his gun. The actor is clearly an extra. He clenches his eyes shut while inexpertly feeling for the handle of his holstered revolver, and pulls it out like he's handling a mushy banana.
As an aside, one thing that peeves me is when a B-grade actor pulls the trigger of a handgun. He/she blinks/grimaces as if afraid the noise is going to hit them in their eyes. My training has me keeping my eyes wide open when taking the shot and observing where the slug lands.