I'm not sure this software is doing anything that matters on a BeBook. You started out with a single-page image in portrait mode and ended up with a single page image in portrait mode. No matter what page size the PDF specifies, the full page will be scaled on the BeBook to fit the actual screen, which is very small (6" diagonal). Things that could effect how a PDF displays on an EInk device include trimming margins and splitting one page into two pages (effectively magnifying what is on the page in the process).
When you hear advice to use small page dimensions for PDF documents, they mean text documents. What matters is how much text fits on each line and each page. Instead of making the overall page smaller with the same font size, you could instead keep the original page size but make the font size much larger (e.g. 26 point instead of 12 point). These two approaches give identical results on the typical EInk device.
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