If this were an alternate universe where Neal and Hook escaped together, then why does Hook not have more grey to age him up the way MJR’s hair looks like it does? Maybe it is just the light in one picture.
We do not know, but it is the leading guess that Pan helped Bae to land where he did to meet Emma. We could be wrong about how that happened.
I think also it could be different sequences they are shooting, that are set in entirely different times and places.
“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass