For a while, RPG Maker games could only run via Proton when using versions 0.49 or older of NWjs. Now, games made with newer versions of NWjs (such as 0.94) can actually run via Proton 9.0-4, however they do not detect any gamepad input whatsoever (such as the SteamDeck built-in gamepad controls). They will receive input via mouse/keyboard or touchscreen only.

Unrelated to Proton, you could try using: https://github.com/bakustarver/rpgmakermlinux-cicpoffs

As a Hotfix, allows you to run it natively on Linux using NWJS as a Proton-like wrapper.

For a while, RPG Maker games could only run via Proton when using versions 0.49 or older of NWjs. Now, games made with newer versions of NWjs (such as 0.94) can actually run via Proton 9.0-4, however they do not detect any gamepad input whatsoever (such as the SteamDeck built-in gamepad controls). They will receive input via mouse/keyboard or touchscreen only.

Unrelated to Proton, you could try using: https://github.com/bakustarver/rpgmakermlinux-cicpoffs

As a Hotfix, allows you to run it natively on Linux using NWJS as a Proton-like wrapper.

The issue with this is that it seems to be a solution for the end-user. I don't think I can deploy to steam like this and have it run for the user. I am a developer trying to make my game compatible with SteamDeck, so my main concern is with uploading something to Steam that will run on the deck out of the box.

For now, staying on an ancient NW.js version (0.49.2) has been the only viable solution, as it does work with current versions of Proton, but it can't properly activate achievements due to poor community steamworks js support for this version (such as no working greenworks or steamworks.js versions), and poor performance compared to newer versions.

At this point, I seem to be stuck choosing between poor performance and no achievements, or SteamDeck/Proton compatibility, since Proton seems to have lost compatibility along the way and never fixed it.