commerce_registration_commerce_cart_order_refresh() not cleaning up all registrations

Currently, commerce_registration_commerce_cart_order_refresh() only calls registration_delete_multiple on registrations that are for products that are no longer in the cart. After checkout the additional restriction of checking the quantity of a product is applied to delete the extra registrations. This works fine until you try to manipulate the cart using rules based on the attributes of the registrations in the cart. Probably not a real common use case, but we encountered it.

The exactly scenario:

1. Create a rule that first removes all add-on items from them cart and then loops through registrations on an order (entity field query using the order_id property) and adds a non-registration enabled product to the cart for every registration where a field on your registration is set to a specific value.
2. Add 2x of a registration enabled product to your cart.
3. Checkout and enter the necessary field value to add the product to your cart. This results in 2x of the add-on item being added to your cart.
4. Return to the cart page and change the quantity of the registration enabled product to 1.
5. Return to the checkout.
6. The first part of our rule correctly removes the add-on items, but then the second part does the query to get all the registrations for an order_id and it gets back two registrations instead of the one that should be left after changing the quantity.

Not the simplest re-creation.