There is a drop down ceiling in the garage over the closet (flush with the top of the door trim). They would have had to go through the door to get to the garage ceiling. It was a poorly designed closet but I guess they didn't think about the type of ventilation needed for newer installations. Oh, and I could not simply use the old gas ventilation pipe as the water heater still uses it.
The two choices that we discussed were to go into the attic above the garage, pipe up to the main attic (2nd story) and out the back roof. The other was across the garage and out the small side roof.
They took it up into the garage attic and straight out the main roof.
Regardless, they will be back on Monday to remove the pipe, plug the hole, re-shingle the area of roof where the flange is and then re-pipe over to the side of the garage to the side roof next to outside wall.