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Calibre does supply a commandline program, called pdfmanipulate.exe, which can be used to trim the whitespace borders but it is not available from any of the GUI menus as far as I know.
On a Windows system (don't know about Mac and Linux), if you have a little technical ability, it is possible to write a short batch file to run it automatically on a selected PDF. You don't actually need to be in Calibre to run this. You could also use a similar approach to get it to loop through a whole directory of PDFs if you wanted. It can be quite slow per book but it could be left to run unattended.
Just in case it's of interest, there is also another free non-Calibre utility, called JPDFBookmarks which, amongst other things, has features which can extract bookmarks from your source PDF and put them back in your cropped PDF
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