He's Bolton's bastard. It hasn't been made explicit, but the implications are all over the place. Bolton sent his bastard to Winterfell, dude outside the walls was blowing a horn at Theon, the X torture is a Bolton thing and suggests sadism, "little bastard". The only reasonable explanation is that it's Bolton's bastard, and what we don't know is how much Greyjoys are involved

And yeah I don't think it's referring to the siblings, but I'm also not a fan of Arya's list. It keeps changing, keeps becoming more irrelevant, and she ain't killing Hound. I've had her killing Mountain since the beginning though. However, that idea was predicated on the contrast between Mountain being enormous while Arya was learning the ways of the Dancing Master with a needle. A small girl using cunning and a tiny blade to kill the biggest baddest motherfucker who ever lived is a good story