Help! Roof coating

Hi folks, I have an old corrugated galvinized barn roof that is nailed down. I hired someone to repair the roof and coat it with fibered aluminum roof coating. Its old and has been coated before, but some rust is starting to come through. In preparation for coating, he scraped the roof well, removed lots of loose nails, replaced them with gasket screws, and tightened up the whole thing. This seems good. But then he placed beads of 100% silicone caulk on other non loose nail heads and small holes in the roof. there are a few hundred beads up there. This is non-paintable caulk, so why would he use this prior to coating the roof!?! Will fibered aluminum actually adhere to and cover that caulk? Seems that, if not, not only would that be unattractive, but the coating would fail much quicker because the hundreds of seams between the caulk beads and the coating would be vulnerable to water- since the caulk and coating dont adhere? This job is not done, he just put the caulk on and wants to coat next week. Thoughts on what to do? thanks Jim