Good news, I've made a 1.5 spoof with EXWY 1.4 that retains the code.bin changes — mostly because that's the only thing I replaced in the 1.1 update. (I had to resign the 1.1 update - anything later gave the infinite waves error, or would not allow the EXWY .code to run at all.
Alternatively, I now think I could theoretically resign the entire pre-patched game to show as version 1.5, and then you could use NTR to load mod updates/changes.
Bad news - it crashes NTR 3.2 when running the regular game and loading EXWY via NTR.
Still going to test if the 1.5 update can be used by layeredFS, then at the very least someone could use a pre-patched full .cia, install the spoof update, and have NTR run on top of the spoof to load the update without any file conflicts.
Actual bad news: the update's files are what causes it to crash. The spoof fully works, but the Lumiose Save glitch and whatever other nonsense bugs will still be present. It seems you can have only have online and the bug fixes, or online and the .code changes.
UPDATE: extracted all changed garcs between 1.0 and 1.1 and compared all the files. Only differences are in a/0/7 and a/2/2 - nothing to do with the .cros at all. So unless the title language UI, text, or language selection has something to do with the Lumiose City save glitch, it's only fixed via the partially-editable update .code. There's no point in keeping the romfs update files except maybe 0/3/6 that was changed in update 1.3.