That it would ask to start APU before pushback, it's normal, so you won't risk ending without a source of power to start the engines by the time the pushback has ended. Yes, there's crossbleed start, but right now GSX doesn't recognize it yet.
Nobody has ever reported a mistake to detect the status of the pitot covers, GSX will ask to remove them only if they are on, I've checked the code and is correct.
And no, custom airplane variable it's not a setting that can be controlled by the GSX.CFG