this guy is alright...

Ok. Solved. The music itself was the issue. As far as i tested, for whatever reason, i needed to re-encode the mp3 file with Audacity with an average quality of 192 kbps. It works now, but i need to do it with another 110 files. Welp. Thanks a lot for your help to pinpoint the problem, at least it wasn't a proton or Steam Deck issue.

Don't feel obligated to experiment or something like that, but i would definetly say "Thanks a lot for your help" if you do. I have tried what you just have posted (game save is cloud save, the custom bgm i'm using it's the same i used on windows and worked in ther, assigned custom track to a random unit and restarted the game) but still no success. Can't help but wonder what i'm doing wrong, or what you did right xD

I had imported my cloud save and Custom BGM folder from Windows, and when I reassigned Devolution Getter's BGM I had to relaunch the game to make it use the new song. I can experiment with it more, if you need me to.

Hello there! Sorry for bothering. I read on protondb that you managed to get working SRW 30 custom music on the Steam Deck by switching proton to experimental. I have tried the same thing but doesn't seems to fix the issue. Did you try anything else before (or after) that could have erm... contributing to the solution or something? Thanks.

+rep friendly