I've successfully cloned an entire disk of one server using Clonezilla live. The only problem is after cloning, the grub menu displays on boot. Grub menu settings are carried over from the cloned machine, so according to my understanding, this should not be happening. I have modified the grub configuration and got the menu down to just one item (linux), but still cannot get the machine to boot without displaying the menu. This is obviously unacceptable for a server build.
All linux machines (server or otherwise) will show a Grub menu at startup. There should also be a countdown to boot to the default option. Maybe Clonezilla ran grub-install & set the default countdown to something like 30 seconds & the default is usually 5 for most recent distributions, so maybe that's throwing you off?