It really is too bad that Bigfoot goes to the trouble of building a waterproof shell, then drills a million holes in it. Doesn't need to be done that way in most cases.
On the Bifgoot 5th wheel I had, water intruded from the awning mounts and ran down the interior paneling, rotting it. The camper I ordered new I instructed than no holes be put in the roof, they have to do some anyway. The one I have now was NOS, so far I've properly fixed all but one of the roof penetrations.
If I had to get into the panelling to fix rot, I'd be very tempted not to replace it with plywood. The BF shell is not thick enough for sufficient rigidity on its own, so the foam and plywood form a sandwich to increase stiffness. Wood is also used in many placed where jacks, tables, cabinets, etc are to be mounted. If it was 1/8 luan I'd replace it with 1/8 G10 fiberglass, a bit heavier but it is much stronger and will never rot. The places where 1/2 ply was used for backer I'd put in 3/8 or 1/2 G10. There are some places where 3/4 or 1 or 1 1/8 were used, that'd be a very heavy piece of G10 so I might stick to plywood. G10 will hold a self tapping screw better than plywood, but being considerably stronger you need to test the size of pilot hole you drill.