FPV Freerider uses Unity's PlayerPrefs to store both the user presets and the controller calibration.
On Linux, Freerider's PlayerPrefs are stored locally at ~/.config/unity3d/Freeride/Freerider
I'm not a linux user myself, and have very limited knowledge in the linux operating system, but I suspect the issue might have something to do with write permissions. Perhaps you could try to double check if you have write permissions for that particular folder.
I believe Linux PlayerPrefs are in xml format, editable with a standard text editor, so you might check to see if you can find and read the Freerider config file.
Thanks, glad to hear that you like the sim although you are experiencing this inconvenience, it would be interesting to hear if you manage to solve this.