I definitely make sure on 2 things :
#1, that the game autoswitches to Mode 2 when I spawn a GV
#2, that I have a manual way to switch modes when needed.
I have my mode 2 set specifically to NOT use the joystick or throttle for anything, as mine tends to drift some. Not a big deal when in aircraft, but a huge pain to have a super small drift on the turret. So I just use mouse/kbd.
And yes, different modes you can set just about everything separately, including scaling and dead bands.
An awesome feature that AH has that I think is a huge step above just about anything out there for the PC. The control customization is tops bar none.