Demand more PDF handling features from Kobo!
Access the PDF on a computer with a screen over 6 inches and with infinitely more features.
Not much you can do on the Kobo at this point if the margins are ruining your ability to see the text. I get this problem as well on PDFs. The zoom feature doesn't shoot in towards the center but shoots in at the left margin which alienates the right margin and renders scooting around on the pdf fairly pointless. You'll just get lot's of margins and some text rather than text and little margin.