It would be awesome if Safari supported the ability to modify the default display rendering of a PDF with a simple query string association.
http://www.domain.com/files/file.pdf#display=twoPage&scroll=continuous
That way a PDF could be initially viewed as the site owner would prefer, but the user could easily change the rendering option on their own.
Just a thought. It could be done using a different PDF engine, an iFrame, some JavaScript, etc. but that’s some potentially brittle work.