Pretty sure that took place in the current timeline. When he asks if there are any guests with her, it's deemed inconclusive. Later we see her in the Spanish village and with the Pinkerton-esque dude come to take her back to her loop before William steps in. It's intentionally framed that way to make it seem as if that scene was a direct result of Stubbs' scene. At the very least, it's left ambiguous.
Stubbs is human.
Also on Reddit people seem to think Hector and Armistice are coming back, but I think not. I read an interview with Nolan and he basically said, yeah, nah. The intended to get rid of a bunch of characters. And the people who made it to the Valley are definitely gone (at least from next season, big picture, he hinted they're coming back).
The nature of this show allows for people to come back within the plot, but it cheapens things to constantly do that. Death should mean something, even for seemingly immortal beings. Especially after the Cradle was destroyed. Flashbacks are always welcome, however.