Reproduced with Inkscape 0.47, 0.48.5, 0.91 and 0.91+devel r14437.
The only combination to differ between transparent document background (picked as fully transparent black) and a black color traced in SVG objects on-canvas is with 'Pick Opacity' and 'Apply Color and Opacity', where clones partially covering document background areas are drawn partially transparent.
Reproduced with Inkscape 0.47, 0.48.5, 0.91 and 0.91+devel r14437.
The only combination to differ between transparent document background (picked as fully transparent black) and a black color traced in SVG objects on-canvas is with 'Pick Opacity' and 'Apply Color and Opacity', where clones partially covering document background areas are drawn partially transparent.