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

Mozilla suggests policies [1] (which, in turn are capable of default-setting or enforcing most prefs and has proper release notes) and has removed a bunch of pages that previously recommended directly editing prefs.js or shipping user.js (which had been changed in backwards-incompatible ways before when the parser was swapped).

[1]: https://mozilla.github.io/policy-templates/