I've committed a change to splivarot.cpp to remove the restriction which stopped our difference/cut/division functions from working on multiple paths.
I was reading the forum post at http://www.inkscapeforum.com/viewtopic.php?f=5&t=20762
and it didn't seem to make much sense, so I did a few tests which I've posted here: https://inkscape.org/en/gallery/item/7216/
You can see we do the most sensible things already and the new functionality enabled by the commit doesn't seem to make a /lot/ of sense as far as I can see, but then I'd like to not artificially restrict the function because someone might find it interesting.
The other hand is that there might be a more common sense way of doing the functions. Maybe by making a union first, or some other thing. But we'd first have to see examples on what users think they'll get when they run these operations on their multiple paths.
Best Regards, Martin Owens