Thats a great point, and thinking about it, you are correct. The one that required a connection was linked to my NNID the other was not linked to a NNID. I'm going to confirm by taking the one that required a internet connection last time and format it again now with the 3 fake wifi. If your theory is correct it should work fine now like the other.
Interesting, I can now format with the wireless switch disabled. So besides the NNID linking there is something else that stops the formatting without wireless switch enabled. Possibly some eshop files? I had been in eshop on both 3ds before the last format.