Run drupal_alter() in advagg_save_data() on the data prior to saving

What about hook_advagg_save_aggregate_alter()? I use it to gzip files as an example.

  $other_parameters = array($files, $type);

/**
 * Allow other modules to alter the contents and add new files to save (.gz).
 *
 * @param array $files_to_save
 *   array($uri => $contents)
 * @param array $aggregate_settings
 *   array of settings.
 * @param array $other_parameters
 *   array of containing $files & $type.
 *
 * @see advagg_save_aggregate()
 * @see advagg_advagg_save_aggregate_alter()
 */
function hook_advagg_save_aggregate_alter(&$files_to_save, $aggregate_settings, $other_parameters) {
...

Thinking I should alter the weight of advag_advagg_save_aggregate_alter so it runs last now that I see other use cases for this. This same hook is used here for S3 #2143913-9: Configure stream wrapper for storing aggregates

The other alt for this use case is higher up hook_advagg_get_css_aggregate_contents_alter(). Given your example use case this is the hook I would use.

/**
 * Allow other modules to modify this aggregates contents.
 *
 * @param string $data
 *   Raw CSS data.
 * @param array $files
 *   List of files used to create this aggregate.
 * @param array $aggregate_settings
 *   An associative array of hooks and settings used.
 *
 * @see advagg_get_css_aggregate_contents()
 * @see advagg_css_compress_advagg_get_css_aggregate_contents_alter()
 */
function hook_advagg_get_css_aggregate_contents_alter(&$data, $files, $aggregate_settings) {
  if (empty($aggregate_settings['variables']['advagg_css_compressor'])) {
    return;
  }

  if ($aggregate_settings['variables']['advagg_css_compressor'] == 2) {
    advagg_css_compress_yui_cssmin($data);
  }
}

Yep :)

If you want to go even higher, before the CSS is aggregated together hook_advagg_get_css_file_contents_alter() would be the ticket

/**
 * Allow other modules to modify this files contents.
 *
 * @param string $contents
 *   Raw file data.
 * @param string $file
 *   Filename
 * @param array $aggregate_settings
 *   An associative array of hooks and settings used.
 *
 * @see advagg_get_css_aggregate_contents()
 * @see advagg_css_compress_advagg_get_css_aggregate_contents_alter()
 */
function hook_advagg_get_css_file_contents_alter(&$contents, $file, $aggregate_settings) {