You are right. It seems to be related to the FPS.
I tested it across multiple Android devices (low end to High end).
On the Desktop the testscene is running at 60 fps constant and on the (sort of) low end devices, the fps drops to ~40. If i set settargetfps AND the physics fixed_fps to 40, the problem is gone. Just limiting the Game FPS doesn't make a difference.
But in my opinion, that shouldn't be the case. Obiously i don't know on which device a player will run the game on. Because of that, the engine should take care of this.
Btw. The Godot Version im running is the 2.1.1 stable (official build)
Thanks Zylann for pointing me in that direction :)
Ps: Weird..... The commenting function in here automatically removes the underscores at settargetfps but leaves them intact at fixed_fps ;D