That is because the current PDF creation processes from Pandoc (either via TeX or HTML) cannot produce a proper Tagged PDF, that is required for screen reader integration.
Your current best bets are to produce the PDF from Word/DocX using either MSWord or LibreOffice, with the option to create Accessible/Tagged PDF turned on or to produce ICML with Pandoc and use Adobe InDesign to produce the Tagged PDF.
I am currently producing Tagged PDFs from Markdown through both of these paths and they each have their own pros and cons...
Future looking, Adobe is actively working with (and funding!) work in the TeX community produce Tagged PDFs - its a ways off, but it will happen.
Leonard