Hi,
The problem is that the fee calculation system is based on a structure of functions and data which supposes that a cart object is used.
The system isn't made to be able to support an order object.
Changing the system to allow for that would be quite troublesome as it would basically require changing the whole payment plugin structure and all the payment plugins.
Now, you could have a developer add that on your website as a quick patch since you probably don't need to support all the complexity we would have to (no taxes on the fees, no percentage fee, no floating tax prices, etc). But doing it properly seems a big project for something almost no one need (even though it might be necessary in your particular case).
So if you really want to do that, I would rather recommand hiring a developer to work on that for you.