So I tested this yesterday and found some weird problems that may be pretty grave. I don't know if it has already been reported, but I'm going to go into detail of what I did and what effects it had:
I currently have n3dsxl with an emunand setup. I installed the TWLapp.cia into both the 9.2 nand and the 11.1 emunand.
I installed the TWLoader.cia in the emunand a setup an old r4i-gold flash card whose firmware have been long gone.
I made .ini for a few roms and tested a castlevania game. It worked fine for a while, but then the audio went silent and after a short while the whole game froze.
"No biggie" I thought, these things are bound to happen with such experimental tools. I power cycled my 3ds and decided to play some smash, but when I tried turning it back on, it would not boot up. After a while, I decided to get the flash card out of slot 1 and the 3ds turned on with no issues.
After it turned back on, I played a few rounds of smash online and then the same thing as when I was playing ds happened: The MUSIC went silent (sound effects were still working) and just as the match finished my 3ds froze completely.
After I power cycled, the 3ds didn't boot up, I took out the slot 1 flash card and it worked again. I tested again if I could replicate the crash and in effect I could. After a match online the music went silent in the middle of my second match and the game froze at the end (just before the transition to the winner screen).
Again, power cycled, 3ds didn't boot up, took out the slot 1 flash card, booted up. I did a third test, this time without introducing the flash card again. This time I could play 8+ matches without encountering any issues.
I found this very weird. It seems like the TWLapp.cia may somehow affect the console audio system causing it to corrupt the system memory when something is inserted in slot 1. It also seems to mess with the boot process of the arm9 when certain conditions happen, like having something in slot 1 after a crash.