I'll leave an account of how I "circumvented" the problem.
First, please forgive my Google Translate English.
I bought a Pokémon Y advertised as defective for around R$50.00 ($9.00). It appears normally on the initial screen, allows language selection, and the initial video plays normally until the "press start" screen. At that point, it freezes. I repeated the process several times, but nothing changed.
It gives me about 39,980 hashes with problems (this is at the beginning of the process; from about 3% onward, it has one or two defective hashes). However, the app in version 1.4 isn't generating the log for me, and the "gm9/out" folder doesn't even exist on my SD card. I've now installed the 100x version to test, but before that, I played around with the files a bit.
One thing I noticed was that mods work. I installed the Portuguese translation, and on the initial language selection screen, I noticed it worked. So I was playing Citra on my PC. I downloaded a ROM from the internet, got the dump from my cartridge, and did some tests. Both accepted the translation, but the dump obviously wouldn't get past the "press start" screen. I tried extracting the ROM files from the downloaded ROM and playing all the content as a mod, and the emulator wouldn't even open any of the ROMs anymore. Then, looking at the files, I noticed one in particular that makes up about 58% of the game's size, and I left only that file as a mod. Both ROMs started working again, and the dump from my cartridge got past the "press start" screen and started the game normally. I did the same on my old 3DS, and it worked too.
This isn't a fix; I just wanted to share it as an idea. I read in previous posts about a Smash Bros. game that started working again, but Dr. Mario couldn't be selected. In theory, just taking his files and playing them as a mod should solve the problem.
Again, please forgive my Google Translate English.