I'd be interested in your workarounds. I've noted this in my feedback on 10.1 beta and there's been no suggestion of any solutions in that forum. Mapbook allowed exporting to pdf through mapbook or through the standard File - Export, and the latter could be used to export at any extent, such as a bookmark. Since DDP uses only the File - Export method and forces that to use its extents, there is lost functionality.
If one doesn't have Page definitions or the similar clips on a layer, then a workaround might be to disable the DDP and export to a "custom" extent, and then not save the project to preserve the DDP. But Page definitions are part of what makes DDP an advance.
I also converted one of my index layers to points and tried moving a couple to get them to produce the altered extents I wanted, with the idea of switching between index layers in DDP, but that was hit or miss in my one attempt.
As a side note reflecting the use of Mapbook as a kind of catalog, it had a nice TOC tab that allowed moving between its pages, being able to see the full page names, and turning pages off or on quickly, which DDP lacks.