My program, Sky Editor, was the first save editor for Explorers of Sky. matix2267 did more research, especially on Pokémon, making Sky JEditor (Sky Editor, in Java).
Both our tools are open source, so I incorporated some of his java code into Sky Editor, applying it for the older games (Time/Darkness/Red/Blue).
If the stats are really stored in different orders in the save and ROM, the developers must have a cruel sense of humor. That, or they were made by different people who didn't directly collaborate.