Hello,
The DOCX output generated by the mergeDocx method is as any other DOCX. There's no reason why a merged DOCX output isn't transformed as any other DOCX unless some warning appears when opening it with MS Word or MS Word can't read it due to missing permissions.
Can you transform the DOCX doing only the transformation? Instead of doing the whole process, if you test only the transformation with the merged DOCX, is it transformed correctly or do you get a timeout too?
If you send to contact[at]phpdocx.com a DOCX sample you are transforming to PDF and returns a timeout error, we'll check it in a test server.
Regards.