Second, according to the comments in the settings.php, you can
initially override any variables stored in the database in the
settings.php file by setting the same variable that variable_get and
variable_set uses:
/**
* Variable overrides:
*
* To override specific entries in the 'variable' table for this site,
* set them here. You usually don't need to use this feature. This is
* useful in a configuration file for a vhost or directory, rather than
* the default settings.php. Any configuration setting from the 'variable'
* table can be given a new value.
*
* Remove the leading hash signs to enable.
*
/# $conf = array(
# 'site_name' => 'My Drupal site',
# 'theme_default' => 'minnelli',
# 'anonymous' => 'Visitor',
# );
The ``bug'' is in conf_init() of includes/bootstrap.ini. The problem
it. This means that $conf isn't registered as a global variable so the
settings are never reserved.