Unable to set Drupal environmental variables using Drush alias $aliases['opendoor_stage'] = array(
    'uri' =&gt; 'stage.opendoor.com',
    'root' =&gt; '/var/www/stage.opendoor.com',
    'db-url' =&gt; 'mysql://someurl',
    'path-aliases' =&gt; array(
      '%dump-dir' =&gt; '/var/www/database-dumps',  
     ),
    'variables' =&gt; array(
        'site_name' =&gt; 'My Drupal siteSSSSSSSSSSSSSSSSSSSSSSSSSSSS',
        'file_temporary_path' =&gt; '/var/www/open_door_files/uploads',
        'file_private_path' =&gt; '/var/www/open_door_files/contentfiles',
      ),
     'command-specific' =&gt; array (
       'sql-sync' =&gt; array (
         'no-cache' =&gt; TRUE,
         'structure-tables-key' =&gt; 'skip',
       ),
     ),
    'command-specific' =&gt; array (
    'sql-sync' =&gt; array (
      'sanitize' =&gt; TRUE,
      'no-ordered-dump' =&gt; TRUE,
      'structure-tables' =&gt; array(
       // You can add more tables which contain data to be ignored by the database dump
        'skip' =&gt; array('cache', 'cache_filter', 'cache_menu', 'cache_page', 'history', 'sessions', 'watchdog'),
      ),
    ),
  ),
  );


I then do the following commands to copy into my stage environment:

drush rsync @opendoor_test @opendoor_stage


and

drush sql-sync @opendoor_test @opendoor_stage --no-cache


Everything copies over fine however the information in the variables array never gets set. What am I doing wrong? I am following the documentation verbatim.
The 'variables' entry in a Drush alias file, or in $options['variables'] in a drushrc.php file will only affect Drush code execution; it does not in any way change the variables table in the database, or affect that way that Drupal runs from the webserver at all.

If you would like to change the values in the database, after sql-sync you could run:

drush @opendoor_stage vset site_name 'My Drupal siteSSSSSSSSSSSSSSSSSSSSSSSSSSSS'


See also sync_enable.drush.inc, which will enable modules and set permissions after every sql-sync operation.  If you often needed to set variables after every sql-sync, you could extend this code to call vset based on the values of entries in the site alias.

POSTSCRIPT:

You might also want to consider using $conf['site_name'] in the destination site's settings.php file rather than change the database value.  This is what most folks do.