I have been developing an MCMS site for a customer that consists of an Authoring and Presentation server in Production. The servers have Map Host Headers enabled. The server are mapped as MCMSAUTHOR for the authoring server and the presentation server as mcms.customer.com.au.
In order to allow content to be migrated between the two environments using the SDAPI without getting a new top level channel in presentation called "MCMSAUTHOR", install this tool (Helicon ISAPI Reweite Lite) http://www.isapirewrite.com/. This tool enables you to rename the top level channel in the authoring environment to be mcms.customer.com.au. Thus migration occurs correctly.
The rules for this transformation would be:
RewriteCond Host: mcmsauthor
RewriteHeader Host: .* mcms\.customer\.com\.au