Fresh out of the oven is eShop Shipping Extension 2.1.7 (you’ll see the update in a few minutes). It has better handling of eShop’s is_shipfree filter. You can create a filter for eshop_is_shipfree and eShop Shipping Extension will handle it correctly.
If you need a hand doing it, contact me through email at vinny [at] usestrict [dot] net so we can discuss the specs and cost. Unfortunately, I don’t have the time to add the UI logic in eSE right now in order to allow users to configure when shipping should be free.