@jamesarm97 I think I've got what you're saying. And I think it's simple to solve. Let's consider that the rotated one is the player2, then your retroarch-joypads/DragonriseInc.GenericUSBJoystick.cfg will look like this:
# ... some configs ...
#input_up_axis = "-1"
#input_down_axis = "+1"
#input_left_axis = "-0"
#input_right_axis = "+0"
input_player1_up_axis = "-1"
input_player1_down_axis = "+1"
input_player1_left_axis = "-0"
input_player1_right_axis = "+0"
input_player2_up_axis = "-0"
input_player2_down_axis = "+0"
input_player2_left_axis = "-1"
input_player2_right_axis = "+1"
# ... remaining configs ...
I mean, you have to hardcode the rotated axis for the player2. I'm not sure if these numbers will work for you, but I hope you get what I'm trying to say. ;-)
Cheers!