How do I get request parameters when using fragment AND query with drupal_goto
I'm guessing you're trying to access the $_GET from the page that's loaded in the overlay (admin/vendor/auth-stripe).  If that's the case, then you've constructed the url wrong.  It should be:
http://mydrupalsite/#overlay=admin/vendor/auth-stripe%3fcode%3dsuccess

That said: where are you actually constructing this URL?  If you're doing it properly, all of that should be taken care of for you automatically.