From what I see, PayPal gateway is the only one that records the fees involved in a transaction. You mentioned that this was possible becasue PayPal records the fees in their callback.
My idea is that there would be a section for the gateway that we could fill in what fee's are required on that particular gateway, then WHMCS could do the math to figure out what the fee should be. For example, 2CO charge .45 for each transaction + 5.5%. We could enter in this info, and WHMCS could calculate it up for each 2CO transaction that was done.
What ya think?