That's because SteamOS has steam installed natively (not via flatpak), and Boxtron flatpak package works only with Steam installed via flatpak.

I think two fixes are needed:

1. Proper installation guide for SteamOS or SteamDeck users.
2. Investigate if we can fix flatpak package to work with native Steam (or maybe create a separate package for SteamOS)

(1) is fairly trivial, (2) is not. I will start with (1).