Hi,
I am on vacation so I don't have access to my copy of the Inkscape source but I believe that both versions are being used, the second through the GTK print dialog where one has the option to print to a PDF file.
I've done a bit of playing around with one of the two versions (print dialog, I think) and I have a fix for the pattern rendering bug (basically, there is one too many transformations being applied). I am guessing that this could also effect the clipping and masking routines. There is some code that I don't understand that seems to try to force the pattern size to be an integer number of pixels in width. I am not sure why this is necessary. It would certainly be helpful to understand the history of these routines.
I hope to have some time when I get back from my vacation to spend on these routines. I think that not having good PDF/printing support is the biggest weakness of Inkscape.
Tav
Tav