OK, rewatched some stuff.
Spoiler!
The Bounty Hunter is clearly working for the changelings. I guess she IS a changeling, which wasn't obvious to me before. It was pointed out the minions on her ship make the same clicking sounds the Intrepid crew changelings do.
But we saw in the scene where she talks to the changelings in charge she's rather reluctant to do so and is being controlled against her will just like everyone else.
So I still think the Borg Queen is the one communicating with Picard Jr. The changelings are after him because they know, somehow, his link to the Borg is a threat to them.
At some point they'll piss Vadic off enough she tells them to go to hell, and then she'll join up with the good guys. That's the only logical reason I can come up with for the BH ship clearly having a Galaxy-Class drive section with a very CONVENIENT slot for a saucer.