2) Yes, wear pants but it has to be a "work pants", not something that you could wear outside. White paint on rubber roof is aging all the time, and as a result the white-ish powder comes off and sticks to your knees (or pants).
4) The only "hidden things" to be worried about are wires. When I drilled holes in the roof for solar panel mounts, I tested each hole with a coat hanger wire before running a sharp 2-inch screw in there. And indeed, once I found the wires under the hole, though they were not dangerously close. Since your screws are short, I wouldn't worry.