It's definitely working fine in both Gen 6 and 7 after my testing...
Please make sure you're using the latest release; the latest commit was pushed ~13 hours ago.
Your CROs need to match the current version. If no update data is installed, CRO needs to be from your game dump. If you have latest update data (1.2) installed, CRO needs to be from your 1.2 dump
Would need to know what you dumped/extracted the game with (best would be dump with GodMode9 and extract with HackingToolkit3DS or .NET 3DS Toolkit), as well as if you're using the latest build of pk3DS or not.
You're a few months late, buddy. This has had S/M support for a very long time.
Make sure you're using the respective code binary that matches the version you have installed.
No Update Data installed -> Load v1.0 code binary (initial release, included with game dump) with pk3DS
Update Data v1.2 installed -> Load v1.2 code binary (obtained by dumping Update Data with GodMode9) with pk3DS
They can be displayed in the OR/AS Pokedex but not the X/Y Pokedex, it always defaults to Furfrou's Natural trim. This is the same with other Pokemon such as Arceus and Genesect. Not a bug.
Dump game with GodMode9 (trimmed) ->extract contents with HackingToolkit3DS or .NET 3DS Toolkit -> Make edits -> Rebuild a .3DS with 3DS Builder -> Convert .3DS to CIA with 3DS Simple CIA Converter -> Install
I can't replicate your issue so it's something you're editing that's invalid... make sure you're using the latest commit.
Your method of dumping/repacking is definitely the issue, as I've rebuilt a Pokemon Y CIA no problem just a few days ago. Follow https://www.youtube.com/watch?v=kvpH_2QBa90
wat
You need to run it from a command-line argument.
Right-click -> New -> Text Document -> Save file name as <whatever>.bat -> Open in Notepad, have it read the following, save, and then run the batch file:
start pkhex hax
exit 0