Maybe Milah made the doll for Bae, but took it with her when she left to remember Bae? Then Bae found it on the ship, a sign that his mother did love him (in her miserable way). Rumpel hasn’t thought about her in years, but he never told Bae he killed her. If he realizes that Hook met Bae (something it is not clear he realizes yet), he might finally realize that Bae found out what Rumpel did to her, and that has got to trigger waves of feelings, that Bae spent years in NL with not just the image of his father breaking their deal, but smashing his mother’s heart. Because if Bae could still love his Papa, after abandonment (though angry), he might have still loved his mother too and not been like “she had it coming, no big loss” as Rumple appears to feel.
“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass