They only indicate alternate reality theory in her nightmare. There is no proof whatsoever the alternate realities exist at any point in the story. It could be that there are multiple threads and only the one she is on now exists at a given moment. We don’t know.

What I find interesting is that they obviously expected people to save Arcadia Bay, given the massively better and more distinct ending sequence - but the choice is split nearly 50/50 according to the stats. They did a good job of setting up a final conundrum, they just didn’t give the ‘second choice’ the love it…

I figured out Loader Bot was the masked man when the game tipped me off. At the moment when Fiona says she recognises his voice I went, “Wait a second!” Before that I had zero clue.