Maybe someone more experienced will disagree with this. On our 99 Burro
, to install the air conditioner, the installers cut parts of the seam down flush with the roof to make the AC fit. We replaced the AC with a Maxx Fan, and covered the now exposed, open seam (about 4-5 inches fore and aft of the new, smaller fan) with roof sealant. Our factory seam doesn't look nearly as nice as yours the whole length of the trailer; it had a bit of a gap. So we actually filled and overlaid it with Interlux waterproof epoxy just to make extra sure it never leaks
, and to keep mold from growing on the exposed, raw fiberglass edge it had. Painted it (and the whole trailer) with Brightsides and put the seam finish molding back on, and it looks fine so far. (I'll update if this changes over the years). So, in summery, you could maybe cut your seam down flush to the roof and just lay the edge of the fan over it (after filling with resin or epoxy or butyl tape of course). There's one idea. I haven't found anything that suggests doing so would compromise the integrity of the shell strength or cause any other problems, but I'm a relative newbie.