So, does this mean I can go online while booted into the emuMMC partition, update firmwares, etc etc and not have to worry about a ban?
Never go online with an emunand, with the same ID as your sysnand. Because chaching your ID is not that simple. Just don't go online. Or at least don't connect to Nintendo Servers. There are special DNSes for if you want to go online with your Emunand.
I never go online with my emunand. Only with my sysnand. Nintendo has different telemetry systems, so you never know what they know of your Switch.