I've had stubborn pickups before. 99% of the time, they would budge, after how little or a lot of time, by gently pulling and rocking the pickups back and forth (assuming the screws were near all the way out/really loose). Sometimes, too, glue or finish can stick to the pickups after a build's completion, believe it or not, which is why I say be careful. This forced me to build patience. I had a Bass Mods bass with Bartolinis, and those pickups wouldn't budge no matter what. They offered to pay for a tech to get them loose, but I didn't like the bass as a whole, so it went back.
I like my pickups quite high, right under the strings (kind of like Billy Sheehan does), to act as a playing ramp, so I need the pickups to have enough foam or whatever underneath, along with long enough screws.