I think that the main issue is that the columns in the PDF aren't identified as columns of sequential text, they are just rectangles. So there is no reliable way to reposition the text so that it doesn't use two columns.

I've seen others propose to replace PDF in favor of more dynamic formats like EPUB. But I wonder if it wouldn't be more pratical to standardize tags and proporties that can be written to the PDFs, so that readers are better able to handle them.