Dave,
Welcome to RVing with SOLAR.
Our Jayco EAGLE 284BHS has a Magnum Truss Roof which gives me about 4 or 5 inches between the roof and the ceiling. Check to see if yours has a truss roof, if so, it will not be an issue.
Don't panic about drilling holes in the roof. if you take your time and put Dicor in the hole, around the opening, on the screws and on top of the mounting brackets you will have no water issues at all. Mine have been on for 4 years now and I check them all the time, and they look the same as when I did the install.
I am sure the others will add to this.
Don