Hello, thanks for playing and reaching out!
The game itself cannot be navigated with a MIDI controller. However, you will encounter and collect 26 presets for the in-game instrument. You can play the instrument while the game is running, or from the Instrument settings screen. Check out the Instrument Unlock cue on the Audio Glossary screen to hear what you’re looking for.
It works great with my microKEY after I allow MIDI access in my Chromium-based browser. You may have better compatibility with the dedicated Linux build. Each instrument preset should support pitch and modulation wheels if your controller has those too.
From my general testing over the years, soundStrider is one of the few games on itch.io which are being truthful about their support for MIDI controllers (notwithstanding explicit virtual instruments or audio toys). I sincerely wish there were more that did this, because MIDI is cool!
Cheers!