If I had the cash (it can be expensive), I'd first update and replace anything that is old on the roof (skylights, roof vents, fridge vent, tank vents), then take the rig to a Rhino Lining or Dave's Permanent Coatings shop. The advantage of their epoxy spray application is that once on, there is no need to ever worry about recaulking again. The only concern is if a branch might tear or puncture the lining, which isn't too hard to have fixed. The two-part epoxy sprays are nice because they cure regardless to exposure to air.
Of course, best of all worlds is an aluminum sheet and the epoxy elastomeric coating, because even if a branch punctured the coating, it wouldn't likely get through the metal.
