Yes, there are some sub-versions of the NAND that aren't supported. Just had a 3ds with 10.0.3.3 emunand(4.3 realnand) which isn't listed in the QR Generator, had to update emunand to 10.5 to get the right QR.
And talking about things that "work"....the lower the firmware-number of the realnand, the more stable homebrew-stuff runs without crashing.
Between 4.5 and the current versions (10.6+) nintendo tried to implement sooo many software-blockades and closed alot of accesspoints the homebrew-stuff is using to gain access to the whole system. As well as alot of encryption.
So basically, with lower realnand your system is easier to homebrew in general, even after hacks are installed.