That is correct. It seems to be the same for the parameter for custom resolutions (-CustomResolution:enabled -r1920x1080x32 for full HD). I ran a shortcut with that command line parameter once, now the game runs in 1920x1080 even if I use a shortcut without any resolution settings. So yeah, the game seems to auomatically save these settings at some point and that's why you need to use the fullscreen parameter rather than just remove the window parameter from the shortcut if you want to restore fullscreen mode.

On another note, I have noticed that the GOG Language Setup shortcut doesn't kick off Run as Administrator. As such, running it and changing the value doesn't actually save the setting as going back in and it is set back to English. If I manually right-click and choose Run as Administrator then after I've saved it then remembers the setting.

For reference, I was trying to get it to accept English (UK) as I want to try to get dd/mm/yy date format.