Antipod caches is a specific kind of mystery that's plotted on one side of the earth, and have the final on the opposite side. These Geocaches are by default excluded from all Geographical statistics in the Profile stats for example.
When Project-GC refers to Antipod caches it generally refers to both the above, and other geocaches with similar issues. Another example is traveling Geocaches, which actually shouldn't exist anymore, but they have existed. These geocaches generally don't follow the guidelines and the effect is that they cause statistical oddities.
HQ maintains a bookmark list containing all these Geocaches, and we just follow their list where applicable.