If strong aim assist is present then that can outperform gyro, but that also can outperform a lot of mouse users to the point that even PC lobbies have mouse users abandoning mouse for aim assist supported inputs. So it depends on the level of aim assist. But, with aim assist removed from the equation gyro is better than joysticks and is surprisingly usable against mouse players despite the absence of auto aiming.

Do you encounter the same issue in desktop mode too?

I tried it on my steam deck and was able to apply my custom template to another game in the normal Steam Deck mode so I wonder if maybe the config is corrupted? Maybe make a simple test config template to check out if it applies to other games is worth trying before making your main config from scratch again.

Simplest way I think is saving the controller layout as a template and then you should be available to see in all games when you go to templates.

I do this for the Steam Controller where I saved a general template to use across games so I don’t need to reconfigure every single part from scratch.