Hey,
I am working with Pixracer, QGC v2.9.7b Release and psp3 gamepad. I am sending commands via wifi. There was a bit funky situation when QGC said communication lost, but arming pixracer and flying with it was no problem.
Here is also short video
I would call it a bug, but I am a bit new in this area as well 
It seems like a false positive, yes. I’ve filed an issue:
Go to rc loss failsafe and change the timeout. Yes it’s kind of bug. Cause even you are not using rc and using gamepad it’s kind of still look for rc. I personally changed it to 30 sec. And my problem was fix. You are lucky cause I had lost the control and lunch failsafe and activated the RTL. I got lucky and returned home safe.
Good luck!!