Selecting default output let's you use a page size, but when I use a5 or b5 as page size, the page size of the PDF is incorrect (something like 0.04 inch). Besides, a5 or b5 isn't correct either, the screen is actually something like 3.6 x 6.1 inch in size. I then tried the Kindle Fire output profile because the Fire has a 1024x600 screen as well. It almost worked, the pages are still too large, but it's by just a couple of pixels.
I'm now trying some Windows programs that can create PDF's from the source images. PrimoPDF for instance let's you define the page size.