If I set custom build options for a file, this is indicated visually in the project explorer by a <> mark on the file icon. If I restore the file options to the defaults (either by manually changing the values back, or by using the restore defaults button on the properties page), the file is still marked as having custom options.
I assume that this option makes the restore defaults button superfluous, as deleting the resource configuration will cause it to revert to its default behaviour.
This still isn’t much help though, if you aren’t sure if a file actually has customisations in the first place. So I would recommend caution when using this option.