I think the problem with xournal is that it cannot ask a file portal to give it access to two related files at once. “I want to let the user pick foo.pdf.xournal, and also give me access to foo.pdf”. So the next best thing is to give it the “access any damned file” permission, and let Xournal grab whatever it wants. You get the same problem with video players - you could take away their permission to open-any-file, but then they won’t be able to pick up a related subtitle file.