Why does Microsoft Exchange Server 2003 and Exchange 2000 Server require you to run /DomainPrep against the root domain, even when no Exchange servers are in the domain?
The Exchange documentation explains that the /DomainPrep operation is primarily used for setting up the Exchange Enterprise Servers and Exchange Domain Servers security groups in each domain that will contain an Exchange server. However, even if you aren't putting Exchange servers in the root domain, you still need to use the /DomainPrep operation on that domain because it will contain some Exchange objects—namely, public folder proxy objects. When you create a public folder, a public folder proxy object is created in the root domain's Exchange System Objects container. The next time the enterprise Recipient Update Service (RUS) runs, it stamps the new public folder proxy with the appropriate email addresses. If you don't run /DomainPrep against the root domain, the RUS can't run. Therefore, the public folder proxies don't get addresses, and you can't post items to public folders.
—Paul Robichaux