You as a developer don't need to tick anything to make it available on Steam Deck.
If you have a Linux version - that will download automatically, the Steam Deck *IS* Linux.
If you don't have a Linux version, Valve's verification will check it on Proton and set it accordingly.
@gamingonlinux Maybe they're only comfortable officially supporting the Steam Deck as a unified hardware/software platform? Not sure if that's a valid excuse but it could be.