I've been trying to educate myself about our printing problem by exploring cairo, librsvg, the uberconvertor and pdf in general. I stumbled across this document entitled, "Achieving Reliable Print Output from Adobe Applications when Using Transparency."
http://partners.adobe.com/public/asn/en/print_resource_center/TXPGuide.pdf
It seems to me that most all of the functionality needed for flattening out transparency already exists in Inkscape. A rather brute force method could be:
1) Replace all strokes with paths 2) Decompose all overlapping objects (this would be an additional boolean op, and it has been requested twice in my recent memory) 3) Replace all area's of overlapping transparency with a bitmap copy. 4) Replace all non overlapping transparency with the resultant color.
Further optimizations would of course be possible. My exploration of cairo and librsvg has only been very casual, but I can't imagine that either of them will be well suited to this sort of decomposition task. But maybe with all of the recent excitement and advancement around vectors a good LGPL computational geometry library will pop up.
Aaron Spike