In my itch manifest, I used platform = (following this guide) for all of my play actions. For whatever reason, this caused my Linux one to always try to use the Windows one and open MyGame.exe.
I also ran butler validate on the .itch.toml and directory and always validated successfully.
Anyway, I decided to never use platform and just modify the .itch.toml to create the correct paths per platform build.
My uname -a comes back as Linux and GNU/Linux, so not sure what the problem is with it. I’m using Pop!_OS, so it’s possible that the itch app is only checking for Ubuntu/Fedora or something like that and not derivatives.