bug#15763: autoload-generate-file-autoloads can put package--builtin-versions in wrong file

[Glenn Morris]

Just found a real example of this problem:
test/lisp/org/org-tests.el: org-package-version fails in both emacs-27
and master. This is because there is no entry for org in
package--builtin-versions. And this is because the entry has gone to
lisp/org/org-loaddefs.el instead of lisp/loaddefs.el.