SMAPI runs using xterm, which is neither installed nor configured in my mostly unaltered Fedora 41 installation. This makes it such that the terminal runs with quite a small font size and light theme regardless of my system settings.

I thus decided that I would try and get the console to launch in my preferred terminal, GNOME's relatively new default: Ptyxis. So I did some poking and after some research I looked through the launch script, added Ptyxis with the correct arguments that will launch a new window with the corresponding command. This command works just fine when I run it through my own Ptyxis instance (it will start a new Ptyxis instance and run the game+SMAPI) but through Steam (using -preferred-terminal-name, but that's irrelevant to the result) it will complain that Ptyxis isn't executable and that it's probably sandboxed or misconfigured.

I thus assume that Steam is the issue here and that it is inherently sandboxing Stardew Valley regardless of my settings. I wonder if anyone reading is able to help me figure this out so that I could potentially open a pull request to add Ptyxis support for those of us running the later versions of GNOME.

I made a Reddit post about this which is just a more in-depth explanation of how I got to this conclusion. Given a short scroll through r/SMAPI I deduced the post was probably not going to get much support there and considered coming directly to GitHub since I'm planning to open a pull request if the solution is sufficiently general