For months I've had both backup options under Dir Comparison > More turned on (Back up files replaced during Copy operation and Ignore backup subdirectory in comparions). Very nice. Except when you try to explicitly compare the backup directory to the "current" one. EDP shows the backup directory as empty because of the second option.
Couldn't EDP make the same distinction as it does for junctions: if the directory being compared itself is a backup directory, then don't ignore it, traverse it.