Actually, I am pretty sure you'd have to update firmware.bin even if you were updating EmuNand. The firmware.bin generation thing is really, really useful for those who don't follow the community, though, and I'm really glad that the feature exists for AuReiNand.
I completely understand about the file transferring by the way: A9LH has an approximate 3-5 hour setup, but the patience to sit/multitask through that varies per person. Personally, whenever I hack someone's 3DS, I just find other things to keep me occupied whenever I'm waiting for Nand dumping/restoring/sd backup/restore.