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It's very hard to tell, especially if it was made shiny in the VC save before going into Transporter in the first place. Most Gen 1 Wild Pokémon can't be shiny, but since the game doesn't record a lot of data and Transporter sets the origin game to whatever VC game it was in right before Transporting, most could technically pass off as Gen-2-bred shinies. There's pretty much always an edge case that makes them technically possible.

Similar bug for another in-game trade pokemon in Pokemon Emerald. Dots, an in-game trade Seedot that you can get in Rustboro city. It becomes illegal when evolved to Nuzleaf and then shiftry. I've also tried using PK files from the living pokedex but the bug still remains. 273 - DOTS - 38BC00000084.pk3 274 - NUZLEAF (DOTS) - 7C7B22DF9399.pk3 275 - SHIFTRY (DOTS) - 7BF7BF07A1E9.pk3

In fact it seems like Mew is the only one to not be transferable due to the event not being reintroduced while Celebi was. Some Pokemon with certain egg moves (like odd egg lucky punch Pokemon) can be transferred as long as it has forgotten those moves. I'm unsure of event moves like surfing Pikachu. If you have a physical cartridge you can buy a device to transfer that data to the VC version before the battery dies. We should all already know what happens then. Hope this helps with further questions.

I had in mind to send my Shiny Mew to my HOME account too, but I forgot to log into Pokemon GO and I have now to restart the 30 day count. I guess my HOME account is going to wait a bit more.