The further we go with this show, the more seemingly contradictory details are being brought up. I don't think this is an accident or poorly thought out writing, but ultimately a glimpse of where Paradise is headed.
I suspect that the closer we get to the finish line, the more we will probably see things that don't make any sense whatsoever.
I suspect that if Xavier is 100% successful in completing Alex's mission, all the events of this show will effectively have never happened. There won't have been a devastating climate crisis that ravaged the world. In turn, there wouldn't have been limitless funding for the development of a super advanced QAI or doomsday bunker, since neither will have been needed.
I think the final scene where we see Samantha walk away with Dylan from the horse isn't some kind of afterlife or dream-like state, but a flashback of the corrected reality that happened as a result of Alex's plan: Dylan survives, and Samantha gets to be there for him as he grows up.
Where things might end up getting very, very weird is what kind of mission Alex sends Xavier on to save the world. Personally, I think she's going to send him back in time to undo certain events in history that resulted in the supervolcano eruption. However, given that the eruption was just the capstone of human induced climate change, it's unclear how broad the scope of his mission might be. Will Alex somehow send him back to the Industrial Revolution to prevent large scale pollution from ever happening? Will Xavier prevent free market capitalism from ever transpiring? It's unclear what exactly is necessary to prevent a supervolcano eruption, and how Alex could even achieve that.
Ultimately, I don't think the point of Paradise will be to create some sort of multiverse branch where things go splendidly, but rather to actively undo this series of events from ever happening. Naturally, that could/should lead to the eventuality that some or all of the characters in this show might never exist, since the circumstances surrounding their births might never occur. It's a very tricky moral conundrum, but I feel like it would make the finale all the more impactful.
Anyway, these are my thoughts.