On a previous customer SR, we dealt with the exact problem that you are reporting to us here.
How are you displaying your PDF file within this section - are you using an iframe?
Below was the explanation given when the issue was previously reported -
"This is not an PRPC issue. The problem is that by referencing the PDF file directly in the iframe in the section, the browser (and the Adobe plugin) which is responsible for displaying the PDF file, is something that we(Pega) don't have control over as it exists outside the web page. It evidently doesn't obey the z-index. You can also try out the same with a simple HTML with iframe with src to open PDF and other frame/div which has overlay, the overlay will always displays under the pdf."
I tried loading the pdf in a iframe and opened the modal via launch local action (in Pega 7.2). It actually worked perfectly well, as a matter of fact the modal dialog appeared above the iframe (PFB screen shot). This is because Pega's modal dialog is positioned fixed hence it will not even particitpate in the document flow and overlap other elements.