The biggest issue with the flashback theory is this timeline of events:
Dolores runs back home to find her (
new) father dead - she momentarily see original Abernathy and starts bugging out
She then "sees" the Man in Black when dealing with Rebus
She has her meltdown and flees
(transition to Stubbs and Elsie)
She wanders into William and Logan's camp, barely conscious
Followed by later, the event with Stubbs being told she's off-loop, them talking about picking her up, and then a guest attempting to pick her up before verifying she's with William.
Now, I know the first part has been passed off as "maybe she's done this twice", but we also know the staff sees her as one of the most reliable hosts there is - see Stubbs's reveal that she's the oldest active host. And the entire presentation of the event makes it seem pretty dubious anyway. It's possible it's trickery, but if so, it's pretty risky and will have to be explained just right later, or honestly I'll feel it's just sloppy audience manipulation. The second part is even
more suspect.
I think the overall issue though is this kind of trick in season one establishes audience expectations. If they are pulling off tricky flashbacks, then for every season going forwards audiences are going to expect some grand twist that affects the entire structure of the season and how literally everything is perceived, which is not necessarily a good thing, and a risky assumption to establish for audiences.
Is the split timeline thing really going to be a twist?
The idea popped up after E2. By now half the fanbase is waiting for the payoff, not the twist itself. The "twist" has been laid out perfectly fine; this won't be a Shyamalan moment because it's been foretold time and time again with various hints and clues.
I think you greatly overestimate how many people are tapped into this theory. The few dozen people in this topic are not by any means representative.