Hidden, required modules cause a bogus confirmation message to appear when the modules page is submitted

Issue Summary

Steps to reproduce:

1. Add code like this to your install profile:
   <?php
/**
* Implements hook_system_info_alter().
*/
function standard_system_info_alter(&$info, $file, $type) {
  if ($file->name == 'field_sql_storage') {
    $info['hidden'] = TRUE;
  }
}
?>
2. Go to the admin/modules page and submit the form.
3. Notice how a nonsensical confirmation message appears on the screen, telling you that you need to enable the Field SQL Storage module to proceed (even though it's a hidden, required module and therefore already enabled).

This bug affects e.g. Drupal distributions which might want to hide certain core required modules from appearing on the modules page in order to simplify it.

I'm attaching two patches, one which I think is correct and one which I almost thought was correct until I realized it causes a regression in certain edge cases. This patch will need tests either way, but I'm uploading both to see exactly what kinds of tests it will need; I'm hoping the second patch will fail existing tests, but I have a feeling it won't :)