It does seem even clearer now that there are multiple timelines. And that the guy adventuring with Dolores is the man in black, which I guess has been obvious for 2 or 3 episodes. There was a specific detail about his marriage in this last ep that makes this a perfect match.
Here's what confuses me, though. We see the behind-the-scenes operations side on a single timeline. Throughout this season, they've commented on specific hosts' misbehavior, interviewed them after key events, or even intervened directly. Was half of that really complete misdirection, and does it even hold together?
Robert Ford said something that should theoretically help us with that — He said that hosts will now and again go astray, i.e. it's been an ongoing thing. Still, I can't imagine things line up properly. If they do, this is a truly brilliant show.