If you ever reprint that book, if you insert a single blank page (The old "This page intentionally left blank") at the start of the PDF (not a whole leaf, just a single page), it'll push the pages along one and put the numbers at the outer edge.
That is a good catch, but after examining the book closer, you do need more than one inserts before certain sections. Sections 1/2 are fine (but only because I used second page as back cover), section 3/4 needs an insert, and section 5 is fine. I just happen to take a picture from section 3 I think. Also probably why I didn't immediately notice the page thing, since it looked fine from my first glance (and I just opened to a random page to snap a pic).
If that site would let me print a hardcover in A4, I might consider redoing it, but looks like 6"x9" is as large as they offer for "Textbook" printing. Just not interested in a smaller size. I looked at a couple alternative sites, but one was wanting ~$100 for a single printing.
Regardless the book has section headings on the outer-edges for nearly every page, so it really is a non-issue for me. If I consider printing another PDF though, I will be a bit more careful about the page numbering.