My suggestion

a) SettingsForm.class.php

class Settings_Form
{
  public static function prepare_db(&$config_vars)
  {
  ...
		// If we have inline permissions we need to prep them.
		if (!empty($inlinePermissions) && allowedTo('manage_permissions'))
		{
			// We'll need to initialize inline permissions sub-form
			require_once(SUBSDIR . '/Permission.subs.php');

			// First Let's take the "global" exclusions
			$permissions_excluded = isset($context['permissions_excluded']) ? $context['permissions_excluded'] : array();

			// Then, if there is any, the "local" (configuration-specific) exclusions
      if (isset($config_var['excluded_groups']))
      {
        $permissions_excluded = array_merge($permissions_excluded, $config_var['excluded_groups']);
      }
			InlinePermissions_Form::init_inline_permissions($inlinePermissions, $permissions_excluded);
		}
  ...
  }
}

b) YourFile.php

$config_vars = [
    ['permissions', 'my_var', 'excluded_groups' => [5]],
];

$context['permissions_excluded'] = array(-1);

Settings_Form::prepare_db($config_vars);

c) Explanation of SettingsForm.class.php

			// First Let's take the "global" exclusions
			$permissions_excluded = isset($context['permissions_excluded']) ? $context['permissions_excluded'] : array();
			/**
			 * $permissions_excluded = array(-1);
			 */

			// Then, if there is any, the "local" (configuration-specific) exclusions
      if (isset($config_var['excluded_groups']))
      {
        $permissions_excluded = array_merge($permissions_excluded, $config_var['excluded_groups']);
  			/**
  			 * $permissions_excluded = array(-1, 5);
  			 */
      }
			InlinePermissions_Form::init_inline_permissions($inlinePermissions, $permissions_excluded);
		}
  ...
  }
}

d) output

$context['my_var'] = array(
	0 => array(
		'id' => 0,
		'name' => 'Regular Members',
		'is_postgroup' => false,
		'status' => 'off',
	),
);

The "-1" entry is not returned because of $context['permissions_excluded'].
The "5" entry is not returned because of 'excluded_groups' in $config_vars.