Any changes in the default preferences don't actually occur in that file, but are automatically pasted through to the user preferences. This saves on copy/paste time, helps new users deal with how the preference system works, and can automate copying comments through, too.
"font_size": 10, to "font_size": 12, in the defaults will actually add that change to user preferences, while leaving the default as it was.
It would be helpful to have a small tooltip or something similar notifying the user of this.
Customer support service by UserEcho