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That, and PC games tend to have literally 0 ideas about any Switch input methods so I very much doubt any game of yours is recognizing a Switch Pro controller.
So let's start form the beginning. What do you observe that makes you think things were not in order?
Steam itself (I checked in Big Picture) always detects the controller as an Xbox controller. Even with the Switch Pro Controller support option checked, it still picks up as an Xbox controller and the A/B and X/Y buttons are swapped to the Xbox layout. Enabling the option to swap them back to the Pro Controller layout doesn't seem to do anything, at least in Big Picture.
Some games use the Pro controller layout. A, B, X, and Y aren't in the Xbox layout, so I don't have to configure a thing. However, other games force me to use the Xbox layout. Some games even load a configuration for a controller not even remotely related to what I'm using.
I only assumed that some games picked it up as a Pro Controller because they didn't automatically reverse the button inputs to Xbox. Which is really where the problem lies - I don't care what controller it picks up as, I just want each and every game to stop reassigning the buttons to a different layout.
Remap this thing in Steam once and for all. There's a page letting you remap all the buttons & axes of any given gamepad. Do that ONCE for this gamepad and go worry-free from there on. I've seen that option to exchange A & B myself but I really found it easier to remap non-conformant gamepads. Did that with 2 different ones, one was similar to what you observe (a couple buttons swapped), the other exposes the right trigger as a button. Needless to say, it was literally impossible to play racing games with it until I've remapped it properly.