Is there any real difference between a link and putting a file in the reference pane? Any different functionality?
Not really, no, excepting the obvious that one is in the text and the other outside of it. If Scrivener links are in the text, you can select some text and create a link to the selection, so you can click through to a reference to, for instance, a character name for information about that character in a separate document. In other words, Scrivener Links associate a link with a specific section of the text whilst a reference associates it with the whole document.