PokEditor VS PokeExpansion

PPRE should be avoided if that's possible. i believe pokeditor is the recommended tool for modifying things like evolution data.

Now there is one tool I didn't mention not because it's bad but I think it's the wrong time to start using it https://github.com/turtleisaac/PokEditor

pokeditor takes pokemon data from the rom and constructs it as a spreadsheet, then re-inserts that data from the spreadsheet after you've made changes. this makes it compatible with existing hacks. it's a command-line tool without a user-friendly interface but it if you're willing to put up with that it is the recommended option for gen 4. it also seems to have gen 5 support but that may be buggy.

editing pokemon base stats and stuff can be done thru pokeditor. it says it has support for gen 5, but there are no gen 5 templates, so... read the instructions closely and use it with caution. there might be other editors for pokemon data out there too.

for instance you said "i'm already using that" but i think that's unlikely. is it possible you're using dizzyeggg's pokeexpansion? what i linked is rhh's pokeemerald-expansion. they are similarly named but not related at all. you shouldn't use PGE with rhh's expansion, and i don't think python is involved in the setup at all.

Sapphire is generally not used as ROM base. If you decide to use Emerald, you can use this instead: https://github.com/DizzyEggg/PokeExpansion.