Have you seen an error that looks like the one below on your Send Pipelines?
There was a failure executing the send pipeline: "Microsoft.BizTalk.DefaultPipelines.XMLTransmit" Source: "XML assembler" Send Port: "some location" Reason: This Assembler cannot retrieve document specification by using this type: "namespace#rootnode".
This is caused by not having a unique combination of namespace and root node (MessageType). BizTalk by default does not like unrecognized messages. The XML Disassembler has a setting to allow unrecognized messages. But what about sending unrecognized messages?
To allow unrecognized messages inside the Send Pipeline, just set the XMLNORM.AllowUnrecognizedMessage message property to True inside a Message Construct shape. This, of course, assumes you have to construct your output message inside the Orchestration.
The statement inside your Construct shape should look like this:
OutMessage(XMLNORM.AllowUnrecognizedMessage) = true;