CJKARR First off, thanks for the feedback.
Regarding your first question, Books can store and launch PDF files if you create a record for the ebook, and add the ebook to the Files section. You can launch the file via the Finder from that screen, but there's no way presently to do that from the main window. Honestly, it's a feature I hadn't thought about.
Regarding your second question, I never intended to allow PDF to be dragged into the cover image fields. This is a fluke and a consequence of me using the default image wells in Cocoa.
(Version 3.0b3)