Chris I did not put much focus on the multisite setups and my list of TODO items is quite big. As soon as I'm done with the next AAM v6, I'll start prioritizing some work that is related to multisite setup.
Couple things here. You may try to use the Multisite None-Member Restriction option that comes with free Multisite extension. This can help to control access to sites that users do not belong to.
Emails, is not a part of AAM, so it is generated and send by WordPress core.
Keep me updated if anything.