Time travel can get complicated. But if the other magical lands still exist and are going about their business as per usual at the same time the Storybrooke events are unfolding, and if Emma’s made a magical hat that can be used to travel between worlds, that wouldn’t actually involve time travel, just travel to a parallel world.
So, for example, if Bae is stuck in Neverland today, still the same age he was centuries ago, Mr Gold could just pop on over and find him. Though he’d need to find a way around the rules of “same number that go in must come out” if he wants to bring Bae back to Storybrooke.