Skylights and dormers
A roof sheds water because it is continuous. A skylight is a deliberate hole in that continuity, and a dormer is a larger one with walls attached. Both work perfectly when flashed properly, and both are the first thing to fail when they are not — which is why the additions this region built forty years ago are calling now.
Why they are the weak point
Water arriving from above has to be diverted around the opening and back onto the roof below it, and that is done with a set of metal pieces layered in a specific order: an apron at the bottom, step flashing up each side woven into the courses, and a head flashing at the top with the covering lapped over it. Every one of those pieces relies on the one beneath it. Sealant is not part of the system — where sealant is doing the work, the system has already failed.
On an older skylight there is a second clock running: the unit itself. Seals fail, glazing gaskets harden, and condensation between panes tells you the window is finished regardless of the flashing. A homeowner sees water and assumes a roof problem; sometimes it is the unit, and telling the difference is the first job of an inspection.
What to insist on at replacement
If a skylight is more than about twenty years old and the roof is coming off, replace the unit while access is free — coming back later costs far more than the unit is worth. Ask that flashing be new rather than reused, and ask specifically what happens at the head, which is the piece that most often gets sealed instead of layered. On dormers, the same question applies at the cheek walls: step flashing woven into each course, not a continuous strip caulked at the top.