The uncertain data will auto-delete itself the more you use the program. The program observes the data on the save and can't know if A^B is (Empty,Full) or (Full,Empty) until it has observed another decryptable state.
KeySAV doesn't generate the entire XORpad when it breaks (it can't), and to help streamline things it can't assume anything. The more you use the program, the more will be unlocked. Try dumping with the boxes empty, then the boxes full, then move different data around and it shouldn't be marked.
As for the met game displayed: there's so much data that it's best that the user just opens it in PKHeX. If you really must have it, create a fork and add it! (In the source there is a class/structure that you can ez get data with)