Instead of foaming the entire roof deck I'm going to ask a contractor to just frame around the HVAC unit with 2x4's and use regular fiberglass batts, to basically make a mini conditioned room around it. Hopefully in a manner that can be taken out easily when the furnace is replaced latter in life. Maybe using 2" foam would work better for that reason.
Obviously the furnace is going to need an air supply for burning, so a new 3' long duct will be needed from the furnace to the outside enclosed wall.
Can this duct be closed off during the summer when the furnance is obviously not running? Obviously if someone forgets to remove it before turning on the heat it will not be good!
I think that is about the best I can do to bring everything into conditioned space short of ripping the old system out and redoing it.