Hello,
The methods addExternalFile and replaceVariableByExternalFile use altChunk tags. This is a 'special' tag supported only in MS Word 2007 for Windows and newer that allows to embed DOCX, MHT, HTML...
As you can read on their API pages, these methods have some limitations (we can't control it behaviour and it's not supported by the conversion plugin). The option matchSource, available for both methods, request Word to preserve the styles as much as possible, so we recommend you to try it.
Anyway, we recommend you to use ther mergeDocx method to merge DOCX documents (http://www.phpdocx.com/api-documentation/docxutilities/merge-Word-documents-with-PHP) and the template methods to use a more avanced approach that allows to keep all styles and it's compatible with the conversion plugin and any DOCX reader.
Regards.