Never happens to me, but is that like if a game you’d override outside the game and play inverted it’d be fine 90% of the time but then it doesn’t make any sense in some menus or maybe the map or whatever?
You have a few options.
On the deck, just use the joystick for one and the trackpad for the other.
Or use either mode shifting or action layers (I never remember which is which) so that behavior changes when you hold another button.
Think kinda like tab vs alt tab, but with like… anything on the controller. Want the joystick the behave differently when holding the left trigger or whatever?