PDF is clipped to media and rotated when imported in shell mode

Attached 51753d39b37413.02355811.PDF has an issue when imported in shell mode into Inkscape and saved as plain SVG.

The issue can be reproduced as follows:
1) save 51753d39b37413.02355811.PDF into c:\temp folder on Windows 7
2) run Inkscape in shell mode and let it convert the PDF into plain SVG
inskcape --shell
Inkscape 0.48.2 r9819 interactive shell mode. Type 'quit' to quit.
>C:/temp/51753d39b37413.02355811.PDF --export-plain-svg=c:/temp/test.svg

When opening a PDF in Inkscape (0.48.2 or 0.48.4), a PDF Import Settings dialog appears. Under "Page Settings" there is an option to "Clip to" certain bounding boxes defined in the PDF. By default, "Clip to" is disabled. This will create a good SVG. Notice in the SVG there is no clip-path elements defined and the image looks good.

However, if the "Clip to" option is enabled in GUI mode, and set to "Media box", then the SVG output from the GUI is identical to the command line output.

Supposedly, the command PDF -> SVG uses the same defaults as the GUI. But it seems that via the command line, the SVG document is clipped to the "Media box" rectangle defined in the PDF, which is not the default in GUI.

One of the ideas how to solve this could be introduction of a new "Clip To" option that would be available in shell mode.