Here's how EFN fees are accounted for in Shopkeeper.

For example, I store one product in UK, and the order was delivered to Germany by the FBA.
Product Settings have this:

(We show same Estimated Fees as Amazon Fee Calculator shows for your product).

So all Pending orders will just have 3.03 EUR.

As soon as order becomes Shipped, Seller Central shows the fee info to us:

So Amazon includes the extra Euro to their FBA fee.

This is automatically picked up by Shopkeeper, and reflected as FBA fee:

We always pull the Actual FBA fees from each order. So you may see a bigger FBA fee in your Sales Overview Reports, than you see in Product Settings, if your order was a cross-country delivery.