Note: This article is based on VMM 2008  and might not apply to VMM 2012 (R2)

Officially SCVMM 2008 does in fact support a disjointed name space. A disjointed name space occurs when the computer’s primary Domain Name System (DNS) suffix does not match the domain of which it is a member. For more information on disjointed name spaces and naming conventions please see the following article:

909264 - Naming conventions in Active Directory for computers, domains, sites, and OUs

So while VMM 2008 does support a disjointed name space, let's take a look at a couple issues you may encounter and how to resolve them:

Note: These scenarios assume that VMM 2008 does not reside in a disjointed name space but other systems including the host and P2V source machine do. For example, the domain is Contoso.com and the SCVMM server resides in Contoso.com but the hosts and P2V (physical to virtual) source machines are in Hosts.Contoso.com.

Scenario 1:
In SCVMM choose to add a host that is “Windows Server-based host on an Active Directory domain” . Enter the name of the server and choose add. You will get the following error.

Hostname.Hosts.Contoso.com cannot be resolve with DNS.

Ensure there is network communication with the DNS server. If the problem persists, contact your network administrator.

ID: 404
Details: No such host is known

To resolve this issue simply check the box “Skip Active Directory name verification” on the Select Host Servers page where the host name is entered. By skipping the verification the host can be successfully added.

Scenario 2:
In SCVMM do a P2V of a physical server by choosing “Convert physical Server”. In the Select Source screen select Browse and find the machine listed as MachineName.Host.Contoso.Com. On the System Information screen select “Scan System”. You will get an error similar to the following.

VMM is unable to complete the request. The connection to the agent MachineName.Host.Contoso.Com was lost.
Ensure that the computer MachineName.Host.Contoso.Com exists on the network, WMI service and the agent are installed and running and that a firewall is not blocking HTTP and WMI traffic.

ID: 3157
Details: The RPC server is unavailable (0x800706BA)

To resolve this issue do not use the Browse button on the Select Source screen. Instead manually enter the machine name in the form of MachineName.Contoso.com.

Note   To view the Microsoft Support version of this article, see Virtual Machine Manager 2008 and disjointed namespaces.

For more information about adding and managing hosts that are in a disjointed namespace, see the TechNet Library article Planning for a Disjointed Namespace.