Magento – Options values of attribute “visibility”

I don't know if this helps you much, but I did something like this using a custom script like this.
In my case I had to read the values from a CSV file, but anything goes as long as you are able to get your data into an array that looks like this:

$values = array(
    array(
        'value'=>'Some value',
        'position'=>'3'
    ),
    ....
);

I also did this for the manufacturer attribute but it works for any other attribute. Let's assume you have the array in the form described above. Here goes:

$manufacturer = Mage::getModel('eav/config')->getAttribute('catalog_product', 'manufacturer'); //get the main attribute
$storeViews = Mage::getModel('core/store')->getCollection()->addFieldToFilter('store_id', array('gt'=>0)); //get all stores
$ids = $storeViews->getAllIds();//get all store ids
$saveOptions = array();//init options to save
if ($manufacturer){
    $_options = $manufacturer->getSource()->getAllOptions(false);//get all existing options so you won't add duplicates
    $options = array();
    foreach ($_options as $_option){ //format the existing options for save
        $options[$_option['label']] = $_option['value'];
    }
}
//read from the array to import $values
foreach ($values as $value){
    if (!isset($options[$name])){//check if the option does not exist
        $index = 'option_'.(count($toInsert) + 1);
        $toInsert[$index] = array();//if it doesn't exist add it to import array
        $toInsert[$index][0] = $value['value'];//set the option label for admin view
        foreach ($ids as $store){
           //empty values for stores - you can also set translated values if you need for each store
           $toInsert[$index][$store] = '';
        }
        $toInsertOrder[$index] = $value['position'];//set the option position
    }
}

Now you should have in the array $toInsert the labels that need to be added, and in $toInsertOrder the positions of the labels. just set the options to the attribute and save it.

$result = array('value' => $toInsert,'order' => $toInsertOrder);
$manufacturer->setData('option', $result);
$manufacturer->save();

I'm not 100% sure on this, I've ever actually used custom options, but tracing back from the template, I think you'd need to rewrite Mage_Catalog_Helper_Product_Configuration::getCustomOptions. I'm assuming the custom option comes from the additional_options field so at the bottom of that function you can just re-arrange the order:

$addOptions = $item->getOptionByCode('additional_options');
if ($addOptions) {
    // switch around the order of the items in the array like so
    $options = array_merge(unserialize($addOptions->getValue()), $options);
}