Does the roof vent have a collar or something? Could you not put an elbow on the pipe and then turn it to make the connection? A picture might help. I've seen round collars that you might be able to use - the flange around the collar would be attached to the roof deck, and it has a fitting to then slide the end of the duct over. Some duct mastic to seal things up and maybe some aluminum tape, and it should solve that issue if there's no collar on the bottom of the roof jack.