I use socket head capscrews (allen head), black phosphate coated.
They stick up a little, but the hex drive is better for driving in with a power screwdriver, and they never get stripped heads.
I use cheap DeWalt battery powered drills, originally the 9.6 volt, and now the Lithium Ion 12 volt which is smaller. You can unzip an airframe pretty fast for inspection, and set the slip clutch low enough to prevent damage upon re-assembly, then final tighten by hand.
The way the slip clutch rattles is good. It allows the philips bit to reset in the head of the screw, reducing the chance of stripping the head.