Would it be possible to write an addon that highlights all modified settings? Most if not all settings have an item Reset to Default Value in the context menu.
This would be helpful when tracking down issues when someone played a bit to much with the settings.

Could an addon be created to highlight changed settings, or would this require to change implementation of blender to adjust all hardcoded default values to the values of the default scene?

Can an hook-method be defined to intercept calls to draw an UI control so that the changed settings could be highlighted in one piece of code?

Apart from that there currently is a bug regarding the default settings.
Unlike a "GUI" toolkit that gives access to the objects drawing the items on screen, in blender we don't really have control of the display - we only say "show a property here", blender then decides how it is displayed.

The colour used to draw each item comes from the theme - keyed, driven or default colour is chosen within the c code that draws the items.