Thank you for your reply.
APM doc mentions HITL HITL Simulators — Dev documentation using FlightGear and X-Plane, but this is for planes only. PX4 doc mentions HITL https://pixhawk.org/users/hil using FlightGear, X-Plane, JSBSim (planes) or jMAVSim (multicopters). I don’t see how inertial navigation is a problem. Like any other sensors, accelerometers and gyros can be replaced by simulated data coming from the simulator (of course the inertial sensors cannot be in the loop whereas you could do expensive hardware in the loop with an optical flow camera by putting it in front of a screen which renders the simulated field of view).
OK, I was just asking this because of Navio+ and Odroid-C1: the most powerful Linux autopilot
I will stick with Pi 3 then.