How about a hex head bolt with a cap that fits over it and snug to the roof? I ask this because when I disassembled this, 6 of the 10 screws threads were RUSTED BELOW the roof line. Which means water is getting in there, and THROUGH the tightened threads of the blind nut. I know a thread sealant would combat this capillary action, but I was also worried about sealing the actual protruding sides of the top flange of the blind nut AND where it meets the roof metal. The flanges of the blind nuts were all SLIGHTLY surface rusted. I wanted them totally weather sealed. The roof panel area meeting the blind nuts were painted and looked perfectly fine.
If you mean the flip-top caps that the bolt goes through the bottom half then the cap snaps over it, I decided against this style because I'd expect the plastic to warp, shrink, dry rot, etc. in the sunlight and heat and, eventually, the caps wouldn't stay snapped closed.
If you were talking about the caps that are basically a disc with a hex-shaped recess to fit over the bolt head, that would work as well but would need to be adhered somehow. They would also sit much higher off the roof than caps snapped into set screws that were flush with the roof line. Thread sealer, such as what is used on bolts that protrude into water jackets in engine blocks should be plenty sufficient as it is (obviously) heat- and water resistant. The flat caps I'd snap over the set screws would have a layer of adhesive sealant (windshield adhesive, etc.) applied to the underside to secure them as well as seal them from the outside. Windshield adhesive is designed to adhere and seal and not weather, so it's ideal. When I press the cap onto the set screw, the adhesive will squish out around the edges. I'd just wipe off the escess while it's still wet. The threaded insert will be completely encapsulated by plastic that's covered by body paint and UV-reflective clear coat as well as adhesive sealant designed for such a purpose. The flat caps would be maybe 2mm high rather than the hex bolt caps which would stand off the body the thickness of the bolt head plus the thickness of the plastic itself. The lower profile would be much cleaner.
"silicone can corrode bare metal" - I never had this problem, been using it like this for for years. I think if you don't put it down too thick and it fully cures it should be fine?
The problem is more common with electronics that are sealed in boxes with regular silicone. The solder and copper are more prone to react with the fumes released by the silicone as it cures. Used in an open automotive environment, the gases can escape. Maybe the problem is inconsistencies when applying the silicone that create air pockets under the cured silicone "skin" leading to corrosion? Maybe you don't apply the silicone excessively thick and you lay a consistent enough bead that there aren't any voids created to encapsulate gases. All I know is I've seen window frames rotted out all around because a leaking window gasket was sealed with household silicone sealant. Though, there are other factors involved such as the alloys in the metal the car body was stamped from and the chemicals used in the production of the silicone itself, all of which may (and likely) have changed over time. I'd still rather play it safe and use purpose-made stuff. Common household silicone sealant isn't as stable in constant outdoor environments as automotive windshield adhesive.