Plugins.txt gets overwritten each time the game starts. In Starfield you have to download this thing called plugins enabler and then you can add mods to the Plugins.txt file like that.
What did you do/what mods did you download in order to get the game to load mods based off of Plugins.txt instead of clearing the contents of Plugins.txt on each launch?
Also, I tried making the file not have write permissions and then I tried making it readonly by everyone except superuser. The game still somehow erased the contents of the file. The game is installed on an ext4 volume.