We don't have the full commentated source code directly from GameFreak with insider knowledge on every tidbit of info. Do you expect us to know everything about every generation save file?
The option is there for people to use for research/modification without updating the program. If someone finds out that setting constant 51 to 5 causes X to happen, you can do the same by repeating the modification on your own save file with PKHeX. If you can't find a list of what does what and it's not in the source code, then it likely is not researched.