At this point I think its clear that the creators don't want you to understand exactly how every scene fits together. Its definitely non-linear story telling. Last night's episode seemed to be pretty clear about that, IMO. I'm not sure it will even qualify as a "twist" or "reveal" at this point after the Lawrence stuff.
I do understand the criticism that the show hasn't really given you a character to care about. At a certain point, the show has to say something compelling about the relationship between the guests and the hosts. I do think that if the fan theories are right, we'll get something that is thought provoking and maybe even moving.
We know that William isn't comfortable treating Dolores as just a Host. He doesn't just see her as an NPC. We know that Delores at some point appears to be moving toward self-consciousness. We know that William is an EVP of a company headed by Logan. We know that company is considering a heavy investment in the park. We know the MiB credits himself for "saving" the park at some time. So what if Dolores's awakening sparks a robot uprising that threatens the very future of the park. And what if William, forced to choose to save his possible investment and status with Delos in the "real world" has to "kill" a self-aware Dolores to do so? He literally has to embrace his role as a villain and the only way to really live with himself afterwards is to embrace what Logan has been telling him. That the Hosts are not human. They're just NPCs. They don't have souls that can be sinned against. And once William convinces himself of that, he becomes a gamer. Someone obsessed with "solving" the game and unconcerned with the cost on the hosts.