Yeah, they were obviously approaching Neverland when Bae broke free of the Shadow's grasp and fell into the drink, where he was picked up by Captain Hook, who one would expect to find off the coast of Neverland.
Heck, it's specifically the sight of Neverland on the horizon that causes Bae to panic and make a last-ditch effort to get away from the Shadow . . . .
I don't think there's any ambiguity there at all.
(Note also that they made a point of establishing that time flows differently in Neverland, presumably to explain how Bae could drop into Neverland back in Edwardian times and eventually wind up in the present day somehow.)