Okay, see those two bits of `org-file-apps' docstring:

`auto-mode'    Matches files that are matched by any entry in `auto-mode-alist',
               so all files Emacs knows how to handle.  Using this with
               command `emacs' will open most files in Emacs.  Beware that this
               will also open html files inside Emacs, unless you add
               ("html" . default) to the list as well.

So (auto-mode . emacs) says to open .pdf files in emacs... but
("\\.pdf\\'" . default) says to open .pdf files using the "default"
application:

 `default'     Use the default application for this file type, which is the
               association for t in the list

Since you have (t . "xdg-open %s"), xdg-open is used.

Yep, it's all a bit tricky...