You can still extract highlights from multi-column PDFs: just be prepared for things to sometime fall out of order. Text in a single column extracts much better (read: much better) than two or three column PDFs. Highlights extract much cleaner from digital PDFs than scanned PDFs with OCR applied. PDF is a fickle file format, so some PDFs highlight better than others: You can also upload PDFs by selecting the PDF Import option from Add Highlights. To import highlights from a PDF, simply email the highlighted PDF file as an attachment to (from an email address associated with your Readwise account).
Yes! But please note that support for PDF highlights is in perpetual beta so you may discover a new bug from time to time (which we will promptly attempt to fix).