Specify destination folders outside of Drupal root using Drush Make
I've noticed how I can get part of the way there without moving the downloaded files around

From my main directory I can run

drush make --no-core --contrib-destination=modules test.make sites


to yield

project_name
  - sites
    - modules
    - themes


then use a standard

drush dl 


to get core and then use custom scripts to symlink core/sites/all -> project_name/sites or something like that. 

There doesn't seem to be an option for --no-contrib or anything like that (probably because there isn't much point)