The Switch 2 Pro, Switch 2 Joycons and NSO GameCube controller all do not work in the base game without turning on Steam Input, but turning Steam Input off is still the recommended way to play the game at tournaments, since SI interferes with support for way more controllers than the base game lacks support for. For instance, I can’t bring my NSO GameCube I use at home to play on a tournament setup because a lot of players use Phobs, which need Steam Input turned off for the best results.
You guys don’t have control over what controllers Steam supports or how it behaves with your game, but you have complete control over how SDL works inside your game natively, please just include suppport for these controllers.