A lot of people have tweeted asking Adam if that scene from Manhattan is still canon as it was not aired and not on the DVD set. No answer thus far. But even if it is, that doesn’t mean that Rumple wasn’t in NL as a boy. He was very young when his father left, probably about 6ish and then went to live with aunt Spinster Aunts, but there is nothing that say he didn’t go to NL during that time and before he married Milah. He wasn’t that young when he and Milah married and decided to start a family. If he was about 45 when Bae was 14, then he was about 31 when they decided to start a family, so let’s say they married at 30. We know that NL isn’t just for pre-teenage boys. Felix is about 18-20 years old. If Rumple lived with his aunts until 18 (assuming that’s the age of majority) he could have gone to NL after that time for even a brief stint. I don’t think his stay in NL was a long one.
Or he even could have gone to NL for a very short period of time while he was a young boy. From what we know of his childhood, his aunts were probably not that loving. If he went missing for a day or two, would they have noticed?