yes you can do that
doesn't make much sense in most cases, but can be quite handy in some scenarios
let's just say for example Big Bad Ninty releases a new firmware with new encryption and gateway would take months to fix that again, you could take your emuNAND, flash it to sysNAND, further update the sysNAND to latest firmware, access eshop, buy games from eshop, play them on latest sysNAND and when you want to play a rom again, you flash 4.x back, launch gateway mode with old emuNAND backup, play your games and switch back and forth, flash on your sysNAND whatever you desire right now and when at some point gateway releases a new firmware, you can just go back to the old 4.x sysNAND and whatever version emuNAND
with a hardmod you can do lots of nice things