Welcome to the Community,
that's probably the main reasons for the warning in the documentation 
Anyway, there are a couple of ways to change the vCenter Server VM's settings. If you have VMware Workstation 10 in place, you can connect to the host on which the vCenter Server VM is registered and manage the settings, another way is using a PowerCLI script to do this. Last but not least you can simply edit the VM's .vmx file manually through the CLI (console or SSH). In this case, don't forget to reload the VM after editing the .vmx file (see http://kb.vmware.com/kb/1026043). In any case you need to shutdown the vCenter Server to change the settings. This can be done by connecting directly to the appropriate ESXi host using the vSphere Client.
André