Yet, it's not WHMCS's job to do this, PayPal will charge 3.4% plus £0.20 (UK Fee's) - it's not WHMCS's job to stop this an charge the client,by using the Payment Gateway, you are trying to support the gateway to get better, not charge more to the client, I would turn away from anyone charging me the gateway fee.

However with your feature, however good, I would prefer this implementation on the add funds section more.