I forgot to mention, in my earlier post, that after you assign a section start and an even page number to the first verso in a document, the first recto can be deleted, leaving you with a doc that starts on a verso with no preceding blanks.
However, by using sections you do lose the ability to carry auto numbering across chapters, as you originally mentioned, and as far as I know there is no way around this. My practical experience only goes as far as QXP 6.52, though; later versions may function differently.
I think mac-nick's right about the PDF bit...if you have separate chapters in Quark, there is no way that I know of to join them during the PDF process, the joining has to be done after.