When we want to import the definition of an IDoc all Boomi can discover is the BasicType that contains the entire IDoc structure, the extension is only a reference in a table and it is only referenced in correlation with the MessageType. So, you can only import BasicTypes.
Please create a Z* BasicType by copying your original IDoc and adding the extension directly into the structure. This way when Boomi discovers the structure, it can pull in the complete IDoc. Make sure to activate the extension before putting it into the BasicType.