Windows 2000 pro and SETPRFDC.EXE

Sorry to say so, but I really could find "THE" answer. I did find some information from "Ask Dr. Bob Your NT and Win2K Questions (May 2000)"
The Setprfdc utility is NT-centric. You can use other methods to control the secure channel establishment and domain controller validation, including #PRE and #DOM tags in the workstation?s LMHOSTS file. However, you mention that you don?t want to use this method, so you might consider an alternative approach, such as setting M-node resolution on the Win95 clients (e.g., through a DHCP scope option or a config.pol system policy file to modify the corresponding Registry option related to the WINS node type).
By default, a client broadcasts to establish a secure channel with a domain controller and authenticate a logon. However, clients don't wait very long for a response. Because of this impatience, a client will often end up using WINS to discover a domain controller, a process that might return the address of a domain controller located acrossa slow WAN link. However, if you set M-node name resolution?which uses broadcasts first and point-to-point name server resolution second (i.e., the opposite of the default H-node type for WINS-enabled clients)?the client will wait longer for a reply. Therefore, a BDC on the local LAN segment will be more likely to respond to the client authentication request. (For more information about this topic, see the Microsoft article "Secure Channel Manipulation with TCP/IP" at http://support.microsoft.com/support/kb/articles/q181/1/71.asp.)

Yes, I know you asked for the usage with Windows 2000 - but as I said could find anything. Hope this points-out some other ways.