[notafox]

prefs.js is modified by browser itself. And it contains lots of stuff by default already.

You can store your custom preferences in user.js file - Firefox will copy those to prefs.js at startup.

From your link:

   The user.js[1] file is optional. If you have one whenever the application is started it will overwrite any settings in prefs.js with the corresponding settings from user.js. 

[1] https://kb.mozillazine.org/User.js_file