It's been years since I had one with a metal roof, but I think I would clean it and leave it un-coated where the gasket seals.
I've only ever had one that leaked. An 84 Coachman. Didn't cause any damage as it ran off the roofing and dripped into the floor out the inside vent and luckily caught it early. The weight of the AC caused the roof to sag around the opening just a small amount, allowing water to puddle slightly. Some are stronger than others and there is a bit of weight sitting up there and bouncing down the road.
Before re-installing, I pulled the roofing staples and added 1/4 inch shims the width of the gasket around the AC opening underneath the roofing. That raised the surface just enough so that rain ran away from the AC gasket.
I have made this modification since then to every camper we have had. It works very well and is something I think they should do at the factory. Even if the roof doesn't sag any.
Also if you wanted to do this, if the AC has a support pad at the far end you'll need to add the same thickness shim there on top of the roofing. I used 3 or 4 layers of scrap EPDM roofing, stuck it down with Dicor sealer.
Joe and Evelyn