When generating the Output Format PDF using Markdown source documents, this message will appear in the generation log:

To publish PDF output using Markdown files, use the format PDF - XSL-FO, which is available for all source document types.

The legacy format called: PDF was created only for publishing Adobe FrameMaker and Microsoft Word source documents, and thus is not available for publishing Markdown source content. If you do attempt to publish a markdown file using the PDF format, you will get a warning message in your ePublisher generation log.