It's pretty idiot proof. The only way to really screw it up is to pull it out while it's working.
Thanks for clarifying. There is some bad info out there, rumors and fake news about what AIO does. Some claim you can disable ABS or SCB, which is complete nonsense. All the AIO does is what one does on their home computer when they customize it. Imagine if you bought an Apple or HP desktop and they refused you to customize your home screen. How lame would that be? Well, that's what Mazda did.
Like you said, once the serial access is done, it renables the USB so access can be done via USB going forward.
Mazda turned off USB access via the update, which is lame but that's what they did. So the software programmers found a way through the serial port in the back. The AIO accesses that.
I did the AIO on my 2016 but that was easier since I used the USB port. The AIO made the Infotainment system work much faster and easier. It's lame how the Nav is locked out once you drive in the OEM firmware. Who locks out the Nav? So stupid but that's Mazda programming.