while it is true that PKHeX don’t support ROM hacks, it would coincidentally (not by design) support saves of ROM hacks that don’t change the save structure.
Anyhow, looking at your file under a hex editor, it’s pure garbage.
All values should not be FF. It means it wasn’t dumped properly. Or maybe you’ve been using state saves, and not actually saved in-game.
Even save editors that supports ROM hacks would not be able to read this. This file may have the size and extension of a Gen 3 save, but this isn’t a save.