The issue is not whether I can see the clicked link in the email, but whether I can track them when they visit my web site after they have opened the PDF...
I can put the PDF anywhere I need it to be. However, when they click the link and the PDF opens in their PDF viewer, they are not looking at my web site, so the Munchkin tracking on the web site will not be linked to the email address I sent the email to.
Of course, I can make a page on web site which has a link to open the PDF, then make the link in the email refer to thsi web page, but this is extra work and extra clicks.