Would a tablet with the PDF on your desk be an acceptable compromise? That's what I tend to do. You can 'flip through' in iBooks by either using the text search

Would a tablet with the PDF on your desk be an acceptable compromise? That's what I tend to do. You can 'flip through' in iBooks by either using the text search, or just hopping over to the contents/notes/bookmarks. It can be pretty effective once you get used to it. You could also pay a relatively small amount to get the PDFs printed and spiral-bound at a print shop. That solves your problem of free-flowing text, plus they lay flat, which is a godsend.