1) The time it takes for the panels to recoup their costs is already long.
2) Now the panels have to be removed and re-installed any time those parts of the roof are worked on. That's expensive. Roofing companies tend not to like solar. You'll have trouble getting a warranty on the work if you've got solar, and likely pay a premium for a company that'll provide one (on top of the much higher labor costs) by finding a company that does both solar and roofing.
3) If work ever needs to be done on the panels, and it doesn't fall under a warranty, it'll be more expensive than ground-level.
4) There's a greater chance of something going wrong with all the above because solar adds more components to the whole system of the roof, aside from punching a bunch of holes in it.
The higher costs and risks plus naturally long pay-off period mean I don't plan to ever pay for rooftop solar again. Wish I hadn't this time.