It might be very handy to be able force a difference to be invisible. That way a user could work his or her way down a long file checking various differences, and removing highlights of differences they have worked through.
Not sure if it could be easily made to work through a save and rescan. If not, then it still could offer some advantage without that ability.
Scanning a forced indifference file pair might be like scanning an unsaved version of the file(s) - something else that CompareIt!3 cannot currently do. Maybe altering the files and being able to scan them without saving them could prove to be equivalent to the feature I described above.