I found that if you load a flight on the runway for example, you have to move the vehicle a bit so it unhooks from whatever the sim has hardcoded to initialize the flight. From my previous experience, setting stuff in the .flt doesn’t matter for some variables like the Battery Master.
If you try to turn off the Master battery when spawning on the runway for example, it will reset to on every second until the vehicle moves. I believe that works the other way as well, if you spawn at the gate for instance.