Mmm. Hmm. Honestly I haven't tried building the linux variant in years. I can confirm what you're seeing, there's the issue of not loading (or applying) localizations from disk, not writing configuration, not executing the actual converter and so on.
I won't be fixing this any time soon. However, not all is lost.
Inside the source folder, CK3toEU4/Data_Files, you'll find configuration-example.txt. copy it to the Release/CK3toEU4/configuration.txt, edit it so it matches your system and options, and run the converter binary manually, thus sidestepping the frontend. The Frontend's only purpose is to generate that file, and once conversion is done, copy the final conversion mod from output/ directory to the eu4's mod flder, which you can also do manually.
I hope this helps.