Without going all the way to implementing themes as in T4213, I think it would go a long way to make basic UI tweaks available to users by adding a setting to the most common apps like Maniphest and Projects to specify custom CSS to be injected into the <style> section of HTML page at rendering time.
Concrete example: to fix the labels not wrapping in the tiles of the workboards (https://github.com/facebook/phabricator/issues/600), one would simply set the CSS override to `white-space: normal;`.
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Obviously such setting might have a disclaimer saying there's not guarantee the overrides will continue to work across releases etc... but it's much much cleaner than having to fork the repo.