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At a certain size (and government departments are absolutely large enough) it makes sense to manage software deployment centrally, from an internal package repository/cache.

Once that’s in place, the process for populating that repository can easily adopt locally modified versions of upstream software: defaults changed, bugs removed, features added, etc.

No one in a big business/government blinks at changing group policies for internal deployment. Changing the code is really very little different once the ability to do so is internalized.