Glitch #1 - You think they would ship it out with the new BIOS. Smart move, I would've probably emailed Supermicro and they would've probably update it.

Glitch #2 - Are you sure administrator access is necessary? I'm pretty sure they don't need to be domain admins. Local admins should suffice. Bert has his staff as local admins.
Local Admin=Admin on that computer only.
Domain Admin=Admin across the network. Highest privileges.

PM me so we can find out if it's necessary.

SBS does hijack the drive. You can partition it after the fact though. I got about 200GB partition from a 2TB Backup Drive and 1TB on my SBS. I like to keep my backups on a separate power supply like those provided with external hard drives. You could get a 2TB External and leave the 1TB as internal storage. Or you can get an external enclosure for the 1TB drive.