I'd like to restore the ability to have pdfs open in a new tab or window. The "lightbox" or whatever is the current default for pdf viewing is creating conflicts with the nav menus and other elements on the page appearing over the pdf content in an embed environment. These sites were built using a WYSWYG editor and embedding the knack code, and they were built previous to this change in the handling of pdf's - when they opened in a new tab and they worked perfectly in that environment.
I am having similar issues. Have you found a way to disable the Fancybox yet? I added a "target=_blank" to all the links, but no joy.
We ran into the same issue! We were embedding in a responsive website that does some floating/resizing and when the PDF files open the website banners/header float above the PDF so you can't read all of it... OR on the file fields, give the option to just download it ...