Files stored in Windchill as content generated by publishing machine are not stored as >PDF files. They are in Windchill as a .PVZ file which is supplemental data and the .PDF in an internal zipped format.
We store AutoCAD files and PDFs in Windchill with the PDF being primary and the DWG as an attachment. Wehen I click on the ODF it opens directly in Adobe, just like a Word file opens in Word.