How can I programmatically configure commerce checkout pane settings?

In Commerce, we have custom pane and checkout configuration that applies to all orders. Per this d.o issue in commerce_features, this is supposedly doable. However, Commerce's default configuration always comes over.

In my feature that Feature creates, it generates the following code:

/**
 * @file
 * my_module_config.features.commerce_checkout_panes.inc
 * 
*/

/**
 * Implements hook_commerce_checkout_panes_default()
 * /
function my_module_commerce_checkout_panes_default() {
  $panes = array();
  $panes = ['account'] = array(
    'page' => 'checkout',
  etc.....
}

All of my panes are there, but they contain Commerce's default configuration, not my custom.

Either the module doesn't work as designed or I'm not using it correctly, either way, I feel this can be done a lot faster / easier programmatically.

All the info I'm finding around .. hook_ .. pane_info_alter() has to deal with changing panes for a particular order or using hook_form_alter to do it on the fly.

I don't want that. In my module.install I want to implement the custom configuration there so that it can still be overridden if needed in the future.

How can I set the global settings rather than have to do it on hook_form_alter for each order?