This has been acknowledged by Altova as a problem with the AltovaXML dll. 
 When using XMLSpy or the command line option the transformation can 
reference a configuration XML file that can point to local copies of common 
DTD/Schema, but there is no mechanism to define this when using the DLL. 
 (Altova Tracking number TTP#36527)

They suggest automating using the command line, but as the Template.html is 
valid already (proven by it being accepted during testing of the 
transformation using XMLSpy) I am happy to go with my workaround of deleting 
the DOCTYPE line.

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