EdwinRR

Pretty much, yeah. PKHeX can randomly generate a legal PID, and sometimes that PID happens to be shiny. The odds are still about the normal Gen 3 shiny rate (1/8192), so you just got lucky.

You could always make one with PKHeX once you have access to a clean save. It only takes a few minutes to fill the PC while leaving the story untouched. I'm not sure if anyone has already shared a save with that exact setup, though.

Yeah, a level 20 shiny Rayquaza is possible. As long as the encounter isn't shiny-locked, there's nothing unusual about it being shiny at that level.

Sounds like the dumper is adding extra data around the actual save. I'd try trimming the save to the raw 32 KB, edit it in PKHeX, then pad/rebuild it back to the original 128 KB format. Someone with the same GB Transferer II should know the exact layout.

You could check the pret and pret-disassembly communities, they've documented a lot of the Gen 1–3 internals. If it's been reverse-engineered, that's probably the best place to start.

If dumping the save turns out to be too much hassle, I'd probably go the GameShark route and read the stats directly. Hopefully someone here knows a compatible dumper for Stadium's FlashRAM saves.

A Pokémon MMO with all regions would be amazing. Co-op story is probably my biggest wish though. I'm not totally sold on replacing turn-based battles with full action combat, but having it as an optional mode could be the best of both worlds.