SoPDF is deisgned to crop the whitespace. If it's not working, it's some kind of bug. Also try PaperCrop. (There's a thread on it here. Too lazy to find the URL to post.)
There are lots of other such tools. Most LaTeX distributions (which is usually considered Free Software by people who track such things) come with a croppdf tool (commandline).
If I'm not entirely mistaken, I think even calibre comes with a similar tool.
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