I wrote an add-on to work around these issues: Instead you get the standard Download dialog with Open and Save. (3) The server doesn't indicate that the file has Content-Type application/pdf so Firefox doesn't follow your rules for handling PDFs. (If you choose either Open option, Firefox will save the file in your system's Temp folder.) Firefox will show the dialog letting you choose between Open in Firefox, Open (in another app), and Save. (2) The server tries to force the browser to download the file by setting the Content-Disposition header to 'attachment'. If you have Open in Firefox set, Firefox will show the PDF in the built-in viewer (and save the file in the web cache with other files collected during browsing). Firefox will follow your instructions on the Options/Preferences page.
(1) The server allows the browser to retrieve the PDF as web content. When you open a link to a PDF, three things can happen: Sorry to make this complicated, but always doesn't mean always because.