Did anyone else notice that as Charlie walked through the under-construction conference room, there was water on the floor and it reflected 01's house in Gamma? In any other show, I'd think it was artistic license. Here, it must have been telling us something. In the next couple of shows I kept on looking at shallow pools of water on concrete, wondering if they were significant.

As for your theories about Brion:
The second and third looks more likely.

As for your Byron theories, I like the second and third the best. It's clear from Charlie's childhood flashbacks that Alpha has been in it's current state (economic zones, etc) for a long, long time. And while Byron is no spring chicken, I don't think he could have totally transformed Alphaverse in one lifetime.

It makes more sense to me that Byron and Boxer have the ability to travel between verses, but something happened to Byron that made him ill. Transfusions from his son are the best solution, but in a pinch getting molecules from a frequent traveller seem to work just as well.
This implies a connection between the illness and verse travelling.

“Blood. Blood’s thicker than water. But then blood’s just a synecdoche for family. And what is family? More importantly, what is a synecdoche?”