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...