I had success in converting Markdown to DITA using the plugin.
I'm attaching a Word Document (DOCX).
<topicref format="pandoc" href="Word%20File%20with%20various%20structures.docx" type="topic"/>
pandoc.process:
[pandoc] Processing D:/projects/eXml/frameworks/dita/DITA-OT3.x/plugins/fox.jason.passthrough.pandoc-master/test/input-markdown/markdown.md
[file-rename] Moving 1 file to D:\projects\eXml\frameworks\dita\DITA-OT3.x\plugins\fox.jason.passthrough.pandoc-master\test\input-markdown\temp\html5\oxygen_dita_temp
[pandoc] Processing D:/projects/eXml/frameworks/dita/DITA-OT3.x/plugins/fox.jason.passthrough.pandoc-master/test/input-markdown/Word File with various structures.docx
[pandoc] Result: 1
[pandoc] pandoc: File: openBinaryFile: does not exist (No such file or directory)
Running pandoc from the command line on the same Word document seems to work for me:
pandoc "D:/projects/eXml/frameworks/dita/DITA-OT3.x/plugins/fox.jason.passthrough.pandoc-master/test/input-markdown/Word File with various structures.docx"