Our app Canteen allows for the collection of mandatory fees. We have many clients using it for collecting the upfront payments on events. Best part is it is impossible to remove it from the cart. Lots of other apps your customer can play games with the cart.
Check it out:
Eventually we found Authorize.net provides a service which allows us to charge a customer second time for the damaged/missing rental item within 90 days of initial purchase. It's a third party payment method supported by Shopify so we're going to use it now. Not sure how it will turn out since we just started, but so far this is the best fit for us. If you heard about something better, please share!