Alright, I've updated my WIP Gen 6 Build VM to successfully build XY (with a bunch of asterisks to that statement albeit). I had to jump through some hoops and "cheat" a little (i.e skip resource build steps) to get it to build, and so far the only kind of mods you could possibly make are code mods (though I'm considering modding the codebase to allow loading bare "named" files outside of the GARCs, to allow people to easily make "asset replacement mods" for the romfs).
https://gofile.io/d/nyGWpDNote: I installed Maya, VS2008, and
space cadet pinball, so with the former 2 plus the addition of the xy repo, the disk usage became a lot higher, so I had to *compress* the VM's disk (which is why all the files have blue names now).
Note 2: kujira_text is just the xy_message repo from August 2012, in case anyone wants to salvage it and recreate the reatil kujira_text repo by hand using the final game's text assets.
Note 3: Though I installed Maya 2012, Game Freak's maya plugin won't work right now for some reason.
Also: In XY's xy_project repo, I have made a WIP "ModConfig.h" in prog\include\ that some source files include, and depending on what is defined in ModConfig.h, certain "code mods" will be enabled.