The enclosed patch allows you to specify --use-existing to use an existing Drupal site at the specified --root. This will allow you to run 'drush make' instead of 'drush dl drupal' to generate your quick-drupal site.
With this patch, I am aiming at supporting the following syntax:
drush qd --make=mymakefile.make ...
I intend to do this with a pre-core-quick-drupal hoo that tests for the --make option, and then sets --use-existing and --root options appropriately before falling through to the regular qd implementation. This way, drush make integration can live in drush make. I don't expect that --use-existing would often be used by hand; maybe it could even be marked 'hidden'.