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Cheat codes tend to generate the incorrect correlation for shinys, so PKHeX’s detection working as intended. Consider this (under category search via PID):

Ok, I think there is a misunderstanding of that feature. It's not meant to give the item to you. The item you can choose here is given to other players that you mix records with ingame. You have two options to get the Eon Ticket into your Emerald: open any other RSE save, to use it as a distributor use my plugin to set the Eon Ticket for Record Mixing go ingame and mix records between that edited RSE save and your Emerald save or: directly put the Eon Ticket into your key pocket set flag 2227

1. Anything that can be transferred from GO can exist as a dumped file. But it doesn't make anything notable enough to need to upload to the site. 2. You answered your own question.

The Eon Ticket was never distributed to Emerald. So which file did you try to import? You can not use the ME3 that was made for RS in Emerald. In Emerald the Eon Ticket is only obtainable by mixing records. This would just put the Eon Ticket in your pocket and set flag 2227 "Can Travel to Southern Island". That's all you need.