Never mind. I created a custom pipeline and that did the trick.
I just dragged an XMLDissassembler and specified the document schema to use. Interestingly this adds a DocumentSpecs value to the Pipeline setup in the send port configuration with a value that looks like:
Namespace.Class+RootNode
Which I tried for the noraml XML receive pipe, but that didn’t work. Not sure what the difference is between my pipe and the BizTalk one.