Once again, I've re-revised my position on how the flashsideways relate to the main Lost U: I'm thinking, again, that the flashsideways follow, narrative-wise, after the resolution of the main story.
The short explanation: If Jacob's Mother was telling the truth when she said that it's bad for humans to capture/harness The Light - and it seems reasonable to suspect that this much, at least, is true - then it's probably also bad that Mother (and Jacob and Smokey) should have it, too. (In brief: Even if they're well-intentioned, there's no reason to think that they're somehow the only people in existence who can't be allowed to have it - that no one else should be allowed to find it or use it because bad things will happen, but these people are an exception. And given all their magical powers, they definitely have it.)
And this is why Jack is a particularly good target to be convinced to accept the mantle - he still wants to fix things, and replacing Jacob essentially makes him the most important fixer in the world. Like Jacob in this past episode, his benevolent intentions make him the ideal, and entirely self-deceiving, candidate.
Why self-deceiving? Because I suspect that The Light should be allowed to leave the island - that the ostensible source of what's good and life-giving probably shouldn't be confined to a cave on an island. So when Smokey-as-Locke finally escapes, it'll be like Pandora's Box, only in reverse, and this is why, for example, the universally bad parents of the main Lost universe will become good parents in the sideways universe, and so on.
And, having written this, I'm at least 95% sure that I'll be proven totally wrong.