I've got qpdf 2.3.0 and it generates a *.xml file for any opened *.pdf file, but the XML files are really small, so I don't worry about it.
Meanie's 200 page zbook3k.pdf creates a XML file that is only 442 bytes.
Most of the other XML files that I have are 422 bytes or smaller.
I keep all my PDF documents in a seperate folder, just for PDF files.
Once in awhile when I delete old PDFs, I also delete all orphaned XML files too.
EDIT, oh, by the way, the XML files store info about what page you are on when you close a PDF document.
It also "remembers" the zoom level for that document.