Management of the X Server

Can I fully manage the X Server with Remote Desktop. Do upgrades, boot off of startup disks and etc.

Yes, you can. I have a server in a remote lab that I have completely managed via ARD for 3 years.
The only issue is, on infrequent occasions it can get "wedged." This has happened to me twice in 3 years. On those occasions I was forced to pay a visit to the data center and manually power cycle the machine (truthfully, I had a coworker on location do it for me).
The new Intel Xserves include elementary Lights-Out Management so you can remotely power cycle the machines should they get "wedged," so properly configured, you should never need to be next to an Intel Xserve to manage it, save some need to actually put media in a drive or something.

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