I've been doing it the same way as @ilikehockeyjerseys mentioned.
I use business/shipping policies. They are set up with Flat Rate shipping for USA/International. The base shipping policy is built assuming the item is duty-free into the States. In the event that the listing is for an item that would incur additional duties I simply edit the shipping policy for that item only using this selection in the drop-down and change the cost of USA shipping to inclusive of any duty owing.

Yes, it requires running every item through Zonos to determine the cost of processing the shipment through them. This adds an extra minute or so to my listing process for unique items. But if you list a lot of things in similar categories then you start to become familiar with it and you can calculate the amount owing without Zonos (e.g. ok this is a shirt made in China, I know Zonos charges 30% on China, plus $2.99, plus 10% of the value of the item in processing fees).
At the moment, I dont' know any better or more efficient way to handle it.
Yes it would be great if Zonos was integrated directly into eBay, but I'm of the opinion that eBay isn't interested in going that route because it would be direct competition to their eIS program that they've invested a lot of time and money into developing.