Sorry I could not load a pdf, so here is the link. You have to open and download the Exhaust Vent specification.

Here is a link that might be useful: Dura Vent Exhaust Vent

The ducting is not suspended from the roof jack and especially not that short a length.
Your approach for locating is correct, but in addition, cut a small hole and adjust from there, allow the ducting to protrude above the foam and use spray foam as a filler.

Use a urethane caulking to attach the roof jack to the foam, then lap the edges of the roof jack with fiberglass tape saturated with the urethane caulking to seal.

Ooohh, very good information! Thank you!

Should we also use fiberglass tape and urethane caulking at the roof jack / duct joint? Or ??

We will anchor the ductwork inside the house using some sort of strapping, but about 4-5 feet below the foam roof, so that is why I am concerned about secure connections.

Many thanks!

All of the duct connections should be reinforced with a quality duct tape, the $12 a rl. not the $2 a rl.
If you are prudent with the size of the roof penetration, just the use of foam as a filler will stabilize the ducting.

I found this Eternabond tape which this site indicates is good for both flashing the roof jack and sealing ductwork. It's expensive, but sounds like just the thing! See the link below

Thank so much snooyb!

Here is a link that might be useful: Eternabond Tape

You are right and for less than $30 in urethane and roofers tape, it's your choice.