hook_theme_registry_alter always overwritten

I'm running into some issues with the Easy Chart module. This is my use case:

In the module, I have a View that appears in a popup. In that popup, I want to use a clean template, so no headers and footers etc. For that purpose, I implement hook_theme_registry_alter, and tell that page to use my custom template that is inculded in the module:

function easychart_theme_registry_alter(&$theme_registry) {
  // Add 'page--editor-easychart.tpl.php' template file
  $theme_registry['page__easychart_charts'] = array();
  $theme_registry['page__easychart_charts']['template'] = 'page--easychart-charts';
  $theme_registry['page__easychart_charts']['path'] = drupal_get_path('module', 'easychart') . "/theme";
  $theme_registry['page__easychart_charts']['render element'] = 'page';
  $theme_registry['page__easychart_charts']['base hook'] = 'page';
  $theme_registry['page__easychart_charts']['type'] = 'module';
  $theme_registry['page__easychart_charts']['theme path'] = drupal_get_path('module', 'easychart') . "/theme";
  $theme_registry['page__easychart_charts']['override preprocess functions'] = TRUE;
}

This overwrite is unfortunately ignored when using the Omega theme. After going through the entire flow, I realized that the function omega_process_page in omega/omega/process/page.process.inc is the culprit:

function omega_process_page(&$variables) {
    if ($layout = omega_layout()) {
      $variables['theme_hook_suggestions'][] = 'omega_page_layout';
      $variables['omega_layout'] = $layout;
    }
}

By adding this suggestion at the end of the entire flow, it seems impossible for me to define a page template in my module.

I checked the issue https://drupal.org/node/2059213 but this does not affect my issue.

I am not sure of a good solution for this, do you have any advise please?