I don't really understand much about this stuff but I assume it's LayeredFS? I have the 'game patching' option enabled on Luma so I assume it's that, no idea what NTR is. Definitely not a rebuilt CIA though.
I changed some stuff in game text, level up moves, evolutions, item stats, move stats, title screen, trainers (for some reason when testing the Elite 4 was still vanilla though), wild encounters, and a lot of personal stats in RomFS. As for CRO, I think the only change is all gift Pokémon having max IVs, other than that, nothing I think.
ExeFS is the weird one, though, I really don't understand it - I did once spend a whole day just trying to get it to work and no matter what I tried nothing seemed to have any effect in the game. Earlier today I just tried recompressing the exefs.bin after renaming .code.bin to code.bin (as someone said on the previous page here) but that didn't work either. However, the first Pokéball Mart in Aquacorde Town is selling only Cherish Balls (which seems to be an ExeFS edit?), which is probably a leftover of Eternal X, the romhack I originally started working on (it was through it that I found out about PK3DS actually), so it seems whatever ExeFS edits were originally made by him/her are still there while my own don't. I've tried editing the shiny rate (originally because I wanted to test some shiny textures I made, but those didn't work either, instead they froze the game, so I gave up on that too) and Mart items, always to no effect.
Is it possible that maybe the saving freeze happens because the games expect some files to be modded when they aren't? That's the best theory I have, but I don't really understand much. If so, how do I put the freaking ExeFS into the game? I tried just about everything - putting an exefs.bin in the title folder, putting the files themselves there inside an exe or an exefs folder, I even tried rebuilding a CIA once but was eventually stopped by errors of all sorts. I'm using a digital game from Freeshop, though I do have the original (Y) game on cartridge (used to have X too but whatever).
(btw, not replying to this too soon as the Breath of the Wild DLC is finishing downloading here and I'm gonna be all over that)