If you use user-overrides.js, it adds your custom preferences at the bottom of the user.js, as the prefs are read from top to bottom, if a new duplicate exist in your user-overrides.js but with a different value the new value would be used as it is at the bottom.
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Have you seen the user.js, you have to change a lot of settings and you cannot keep up to date with them, secondly Arkenfox prefers you to go over their user.js by your self and their updater script has the -c flag to show you the difference between current user.js and new user.js
Overall it would be very difficult to manage something like this on our own as most things are not visible on the settings page of Firefox