And yes Some Pig No Doubt, definitely multiple timelines, so we probably have seen human Bernard in a flashback, and I'd even go so far to say we've seen human Bernarold with Dolores
Like I said:
Current time - Bernard with Ford, Theresa, new narrative, board members, MiB, some Dolores, Terminator Maeve ~30 years past - William and Dolores, possibly even Rancher Maeve and daughter ~35 years past - Bernard and Dolores
I think William's little monologue in the train pretty much confirmed for me that he's the MiB. I'm really interested in "how" he becomes the MiB, though - I'm betting Dolores turns on him in some way during the uprising. The MiB is way too callous and bitter toward her in particular for her to merely be a lost love interest that could never be.