Does get_defined_vars() show variables defined in variable_set()?
get_defined_vars is a PHP function, not a Drupal function.  It basically shows you all variables that are in scope.

Drupal variables set by variable_set are not automatically within scope.

Variables are stored in global $conf; but I don't recall if non-variables are also stored here.

If you install the Devel Module there is a page for viewing and editing variables.

EDIT:

Curiosity got to me.  The variable editor in the Devel Module queries the {variable} table and not global $conf; to build the form of all available variables, so that suggests that is the proper way to do it.