If a guest damages exceed the security deposit is there a way to charge their merchant account the extra damages through OwnerRez?
If you have a card on file, which you will for any credit card based booking (not PayPal), you can charge it at any point on the Transactions tab of the booking. We leave all of that between you and the guest and don't lock you into any certain payment schedule or cancellation policy.
However, be careful to get an agreement in writing from the guest before you charge, whether that be in the renter agreement or ideally an admission of damage after the fact and agreement to pay. Without that agreement, you'd likely loose if the guest were to do a chargeback, and then you'd have to follow up in small claims court.