Yes. Apps like ShipStation, ShippingEasy, and Shippo, work perfectly with Multiship with no change to your current order fulfillment process.
Multiship automatically cancels the initial order from your customer, and then recreates orders per shipping address. This initial 'canceled' order is purposefully not exported to your 3rd party shipping app, as it is not meant to be fulfilled. Only the orders meant to be fulfilled are exported, ensuring compatibility.