This has confused several people I know. In fact it really spooked a good friend of mine. I must remember to make it a point to clarify what is happening and where it is happening. The updates are to the firmware in the Airport Extreme Base Station and Airport Express base station in your WiFi network and do not install or change anything on your computer, your computer's firmware, operating system, or any applications on your computer. The only changes are to the network devices.
The Airport Extreme and Airport Express reboots are performed automagically by the installer as part of the installation process. Simply run the installer from within Airport Utility and the rest is automatic. It does not even change any of the settings in either device.
