SoPDF is not designed to handle multi-column PDFs. The 2x options were designed for splitting a single page vertically (and then rotating for viewing on the reader in landscape), not for splitting up columns. You might have better luck with something like
BRISS.
However, if SoPDF manages to cut your multicolumn PDFs in the right place (this would be luck), I suppose you could use
jPDFTweak or
pdftk to rotate them back upwards, but I bet it would take another run through SoPDF to get rid of the middle margins.