A resolution to all issues. Gamenaut over in the FE discussion forum on Steam had this to say:
On Linux desktop, the solution is to Alt-Tab out of the game and get back to it, then it works (not sure how to do that on the Deck, though). The only way for the game to run without this workaround is by running it on Proton 4.11-13. Also, it's needed to delete the SDNXLFonts.dll file in the game's folder; otherwise some texts won't show up.
It's worth mentioning that there's a bug going on for a while (in some Windows installs and Linux with newer Proton) in which the game crashes on loading a save, but there's a workaround for that in this thread. By running the game on Proton 4.11-13, you won't have this issue, but the performance there is quite poor (it uses OpenGL instead of Vulkan, which the newer Protons uses).
Summary for the best experience and performance on Linux:
* Delete the SDNXLFonts.dll file
* Run the game on Proton Experimental (Alt-Tab needed after boot)
* When loading a previous save, start a new game, go back to the menu and load it
After that it's a smooth sail. I know it seems like a lot of work, but it's worth it. The game runs much smoother than on Windows after that.
I've verified that this works as well and that the current versions of Proton Experimental and GE Proton still retain the bug. I simply moved the font file to a backup folder and the text correctly displays. Using Proton 4.11-13, the game can now be played normally from within the Deck interface.
Is there any shot of a Stardock dev getting enough time budget to work through this issue to make the game playable by default, possibly upgrading the game's verified status to "playable"?