I have been at a few client sites that had required that we use cusom namespaces for their HL7 interfaces.
This is all well and good, but what is not mentioned is that you have to have the BTHL72XCommon project deployed, because the acellerator absolutely requires it to be deployed to handle the MSH segment.
The reason why this is the case is because the pipeline component only looks for the default microsoft target namespace (http://microsoft.com/HealthCare/HL7/2X). The implications of this are: if you want to make changes to the format of the MSH segment, you only can do it with one schema.