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You can get Custom firmware on the Switch, but yeah if you don’t have a Switch it’s fine too. Just saying.

Yep, the transfer pretty much recreates official hardware transfer. Since you can trade the Pokemon to any game and any language (minus Korean in gen 4), the language of the carts don't matter in gen 4 or 5. The 3DS region information is set by the region of the 3DS that transfers the Pokemon from gen 5 into Bank. The only minimal thing that PKHeX transfer misses is nickname trash bytes from gen 5, but since you're transferring a Japanese Pokemon from a Japanese game that's not needed anyway.

ah fair enough~ hmmm, if you don't intend to ever have the mons on actual consoles, then the note doesn't really mean anything.

I missed this earlier. I don't think anything I said was related to the Game Shark All things considered, I got mine at a nice point in time (Gen 3) but back then it felt pretty late to me (wish I got it in Gen 1/2 and messed with all kinds of stuff) I don't don't deal with his project. All I can say is that he is aware and would update it when he finds time to do so. Not sure what version you're trying to do the Kyogre thing on, I assume SoulSilver. Anyhow, various steps in the spoiler below, click on it to open it:

Not download Gold. That sounds like piracy. I meant select Gold as the origin game in the Encounter Database window. I could attach a few photos if you can’t figure it out