I mean that’s mostly because a separate Nintendo controller that wasn’t highly specialized for Nintendo games specifically is mostly a new thing.
We’ve had Xbox controllers and Playstation controllers for 2 and almost 3 decades respectively, and Nintendo games are the most targetted for emulation so of course there will be a lot of community effort put into mods for those.
Meanwhile your options for Nintendo controllers practically boiled down to Wii controllers, the Wii U gamepad, the NES controllers, the N64 controller, the consoles themselves like the 3DS/DS/Gameboy, and some others. Most of them are part of the consoles themselves so are out of the picture, the Wii controller is just not suitable for other consoles, the NES controllers don’t have joysticks, and the N64 controller has a single joystick.
The Switch controllers, which are relatively new, are really the only ones suitable for emulating other consoles’ games, and you can use the Switch controller to comfortably emulate many non-Nintendo games now.
Considering that, another important factor is that since the Switch controllers are more recent, they’re less likely to have been adapted to older or more obscure games especially, since to do that people now have to go do “back in time” modding for old games years or decades after their release. And since most modern non-Nintendo console games are available on PC natively and aren’t emulated, there’s really no incentive to make QOL mods for people using Switch controllers (or any other kinds of controllers for that matter, including PS & Xbox controllers) on newer titles.
It has nothing to do with the button layout itself, it wouldn’t even make sense for that to be the reason. People will use whatever controller they have available, so people who play Nintendo games most often will likely use Nintendo controllers and people who play the Xbox most often will likely use Xbox controllers.