If Alice went through a rabbit hole in our world and came out into Wonderland….then the rabbit hole should still be in Wonderland. The way Alice gets back to our land is pretty unclear, especially in the movie where it’s almost like she was dreaming. Maybe in the end there is no way to back our land from Wonderland. One time only trip. So, Alice and Jefferson fall in love, but she can’t get back home and even as a portal jumper Jefferson can’t help her. They keep trying to get her home but at some point it has dire consequences and she dies because of their efforts and he swears to give up portal jumping and raise their daughter instead.
Random theory that I just spun out while typing this comment. 🙂
Another option with that is that yes, he found her in Wonderland via portals, but took her with him, leaving behind whoever else he had brought. (Perhaps another portal jumper, like the White Rabbit?) and they get married and she gets pregnant. They keep going through portals to make more money, and then she goes into labour prematurely while they’re in another world. He’s forced to leave her behind to take Grace… And when he returns for her he discovers that she’s dead.