I am also interested to know if there is a way for SCCM to use FQDN. Our environment has many child domains. We have to add each domain to the "Append these DNS suffixes (in order)" section of TCP/IP settings of your network adapter. I think (but haven't been able to find documentation) that there is a character limit to this list.
We have to frequently change the domains in our list so I keep the most common ones and change the odd ones when needed.
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\ControlSet001\services\Tcpip\Parameters]
"SearchList"="CommonDomain.org,YourDomain.org,MyDomain.org,OddDomain.org"