You have two options:
1. Find the widget class that displays the option.twig template (it is classes/XLite/Module/XC/ProductVariants/View/Product/AttributeValue/Customer/Select.php), "
decorate" it from
your custom module and make it use your custom template instead of the original option.twig
2. Use the ability to
define custom template directories and make X-Cart look for the template in your directory first.