Updated chart. Seems to still be holding strong, but I might've missed something during the new episode that disproves it.

Here are the current points of contention against TTT (Two Timelines Theory), alongside possible responses for them:
>TDOTS a S&B were meant to be one interconnected movie
That is true, however, all it proves is that TTT wasn't always the intention, but there's nothing stopping Tamers from having changed course mid-series.
>Flawless reflection
Could be a remnant from before Tamers changed course, since this was the first episode after the two movies, and we know he finishes episodes well before releasing them. Could also just be an easter egg. Still the second biggest point against the theory.
>Apple Bottom flashback had scenes from Twixie Timeline
Can be easily explained as a simple fourth wall break. It's not like he directly mentions any of the events, so he's probably not even aware they happened.
>Apple Bloom being aged up during Porta Potty
Single biggest point against the theory. The only explanation I can think of is that it was a genuine mistake and Tamers just forgot that didn't happen in said timeline. The only reason why I don't count this as outright theory-breaking is that AB is a very minor character in the grand scheme of things, so it's more believable for a mistake to have happened with her.
>Twilight's window in the gay wedding episode
This is a pretty weak one, since nothing says similar enough events can't happen in both timelines. Twilight's house doesn't need to get labuboom'd for the window to be replaced. It could also genuinely just be a throwaway line.