Any chance for alter system settings form via hook_form_alter?
Do not forget at the end of your hook_form_alter() or hook_form_FORM_ID_alter():

$form = system_settings_form($form);


If you don't want to add the "Save configuration" button, you have to add your custom callback submit with $form['#submit'][] = '_my_callback_form_submit'; and : 

function _my_callback_form_submit($form, &amp;$form_state) {
  variable_set('my_variable_name', $form_state['values']['my_variable_name']);
}