So effectively, I am assuming that you run this command:
sim_vehicle.py along with some arguments to run a simulator.
Even in our case, the backend simulator that we are working on to get APM SITL support up and running is the same simulator and NOT a gazebo based 3d physics simulator. So,
yes this is indeed possible. But if I am right it won't solve your purpose. Because, if you write your code using FlytAPIs, you can ofcourse test your code in our simulator or visualize in APM planner. But if you want to control your drone using mavproxy via APM planner, it bypasses FlytOS alltogether.
I hope my answer was clear enough.