Over in the “Mr. Gold’s Threat” thread, I suggested that this reunion might be the thing that prevents Emma from killing Gold. Without it, I think the threat Gold made against her family at the end of “In the Name of the Brother” might convince Emma that she has to act to protect Henry and her parents and take advantage of his temporary vulnerability while he is outside Storybrooke and without his powers. Phee suggested in that thread that seeing him so weak and vulnerable in the outside world might change her view of him and give the two of them a chance to grow closer. That could make her more sympathetic to him than Bae/Neal will be.
If Neal is Bae, I’m hoping we get some backstory on how he grew up in our world. Given what he went through, and the fact that he was alone in this world, it would not be surprising that he turned out to have the troubled past we saw in “Tallahassee”.