Thanks for your inquiry. The MarkupLevel of StructuredDocumentTag is correct for both documents. Please check the both documents in DOM. You may also check this in document.xml of input documents. See the attached images for detail. Please read following documentation link for your kind reference. https://docs.aspose.com/words/java/logical-levels-of-nodes-in-a-document/
Please check following code example and let us know if you have any more queries.