Well...at least with the motors I have seen, that's the way it is - the pinion needs to be high-up on the motor shaft. It's hard to say how you could mod that motor to keep the pinion from slipping, without actually seeing it. Since you already have a flat spot, how about making it deeper into the shaft? I didn't like the idea of Loctite at first, but it really is the way to go with these types of motors.

I have the 'cool red' brushless from Hobby Lobby - it's the same as the blue shogun brushless motor. It also has a smooth 2.3mm shaft.