How do I get Drupal to preference one of a module's .tpls over another?
Update the modules weight in the DB.

This code is for a custom module, when enabled:

/**
 * Implements hook_enable()
 */
function YOUR_MODULE_enable() {
    db_update('system')
    -&gt;fields(array('weight' =&gt; 1))
    -&gt;condition('type', 'module')
    -&gt;condition('name', 'YOUR_MODULE')
    -&gt;execute();
}