That conflict checker may need to be updated, it says all of my files conflict with themselves.
This program only appears to check the Instance ID of a ResourceKey to see if it conflicts, which is going to cause major problems on packages that have multiple ResourceKeys that use the same Instance ID (as in the case of hair, and, in fact, a lot of the game files, as well as Store items).
I would seriously suggest that it be updated to check the Type and Group IDs as well as Instance, because otherwise, the report has a lot of false positives and people, as can be seen from the comments, can get very confused.
So it may not be the best thing to use it to check for conflicts.