It doesn't. You don't need any patched FIRM in the aurei folder anymore. firmware.bin is only if you use NTR basically, it's fully optional. There's no code for loading any other firmware file.
I meant like, when you have already installed a patched TWL_FIRM or AGB_FIRM on your NAND.

Anyway, it actually works! The GBA splash screen is there even when my AGB_FIRM is modified. Same for TWL_FIRM stuff, I thought that it would have some incompatibility, but it's fine.
Boot time is also very fast, it's just amazing. I guess it has the same speed than an unhacked 3DS now.
Shame that I can't help a lot with testing though.

Btw have you thought of getting rid of the "aurei" folder or renaming it to "payloads"? It's almost useless by now, I think? (Besides the NTR FIRM and the config.bin, I guess)
No need for the patched agb firm now?
AuReiNAND had on-the-go AGB_FIRM patching for a while.
