Previously, "Personal Docs" was a flag set on MOBI files. Unless you manually set this yourself in the metadata, the only way for a file to be a "Personal Doc" was if it passed through Amazon's email conversion. MOBI or TXT files you copied manaully onto the Kindle would show up under "Books". (Also, the Archived Items directory showed up under Personal Docs.)
On the DX, PDF files you copy manually onto the Kindle show up under "Books". This breaks the previously established paradigm. Unless Amazon adds a way to "tag" a book on the Kindle as either Personal Doc or Book, then you're also going to have some items miscategorized. But I really don't like all PDFs being considered Personal Docs; I'd be happier confining that label to Amazon-converted files until they implement a way to tag the books from the Kindle.
As to downloading PDFs, yes I mean in the web browser. It has nothing to do with the email conversion process. It's just an assumption that was made for previous Kindles about what sort of files the Kindle can natively read and thus download. It's just another indication that the PDF viewer was just slapped onto the Kindle without any integration with other software.