Well. It may that you ran into a trap here. Some defaults can just be changed by modifying the source code. Some things are not stored in the User Prefs or the startup.blend . Every little default is dealt different. Ask the Blender devs why …
But i will check.
EDIT, interesting, for me it works just fine. It keeps the milimeters when saving the startup.blend.
I am a bit clueless what goes wrong at your end :/
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