Hello Lance,
a. We believe that it does work with WordPress Multiuser. I have personally tested it, but I do need feedback from real users like you. You can always install our free Akeeba Backup Core for WordPress through WP's Plugins page. Take a backup and try restoring it elsewhere, e.g. a local site.
b. Akeeba Backup for WordPress gets its database connection information from WordPress itself. I suppose that plugin circumvents WP's configuration for the blog network. This means that Akeeba Backup for WordPress won't know about the other databases. HOWEVER! We already have made provisions for such a case :) With Akeeba Backup Professional for WordPress (the paid one) you can define "additional databases". You just give it the connection details to the databases you want it to backup up and it does. It also restores them just fine.
What might not work in this scenario is restoring to a different domain, subdomain or subdirectory. This requires us to go through the database of each site and change certain settings and URLs in a lot of database records. Since the restoration script will not know which blog is inside which database it might not be able to do that. In this case we can work with you to try and change our software to do that.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!