> Create an Elisp file such as
>    (defvar foo ?()
> and try to run `update-file-autoloads' on it.  This will fail with an
> unbalanced parenthesis error.  However, this is valid (albeit
> discouraged) Elisp code.

Yes: don't do that.  Use (defvar foo ?\() instead.
This same error will appear during interactive editing of that code.