I guess I'm not understanding your setup. Why are your endpoints not 100%? The naza is a fly-by-wire system, so your four main controls (T/Y/P/R) should all be -100 to +100 under normal conditions, and command the Naza inputs the full range, and centered sticks should command 0. You also need the full range from -100 to +100 to command the Naza to arm the motors.
Obviously, you'll might want to program some scenarios on the transmitter limit the full range, but that would only be to limit the authority of the controls in that direction. For example limiting yaw to -30 to +30 for finer control of yaw motion while shooting video on a 2-axis gimbal. Or for aileron, you might have a a scenario in the transmitter for limiting roll authority. Is that what you have setup? Do you have a special case where you aren't commanding -100 to +100?
But yes, whatever you setup for your endpoints will affect all Naza modes: GPS, ATT, and MAN (those aren't transmitter modes). And again, for commanding the CSC procedure to start the motors you need the full range, and for running the Naza input calibration you need the full range as well.
Can you explain your setup a little more?