How to properly use a custom them during the installation process

Without a custom theme, the installation completes nicely.

I was clueless in how to activate a custom theme for the installation process, so I copied commerce kickstart's method and have probably left something out:

function commerce_kickstart_install_tasks_alter(&$tasks, $install_state) {
...
_commerce_kickstart_set_theme('commerce_kickstart_admin');
...
}

function _commerce_kickstart_set_theme($target_theme) {
  if ($GLOBALS['theme'] != $target_theme) {
    unset($GLOBALS['theme']);

    drupal_static_reset();
    $GLOBALS['conf']['maintenance_theme'] = $target_theme;
    _drupal_maintenance_theme();
  }
}

I've revised my question: how to properly use a custom theme during the installation process?

I also have a secondary question: what is happening to the system table between the database creation step, site configuration and the last step. Why does the system table get "flushed" and rebuilt again? It appears this isn't happening during the commerce kickstart installation process. I'm going to try to figure out why.

I simply ran the following query at different times during the installation:

select filename, name, type, owner, status, bootstrap, schema_version, weight from system;

When the database is first created, the system table (in my case) has 270 rows; after the Site Configuration step the number of rows drops by about 100; after the last step the number of rows pops back up to 270.

The base theme info is being left out of the system table.

I don't know what magic has been done in commerce kickstart to avoid this situation (for they are also using a base theme), but here is my quick fix:

  if (in_array('install_bootstrap_full', $install_state['tasks_performed'])) {
    system_rebuild_theme_data();
  }

I could probably check if the zen base theme info is in the system table first before calling system_rebuild_theme_data, but it works.