Hello Alex,
The payment gateway always should have a priority on fees, otherwise, why be a payment gateway. For example, if I run a multi-store and vendors add their products similar to eBay to sell or barter, I should have the option to charge or not to charge a fee. Woocommerce should not override my choice. It is a critical feature. Otherwise, I have to use another plug to add a fee and that would make no sense.
Regards
Adonis