OK, looks like that won’t work in this instance. I’d like it to automatically calculate a percentage fee on the subtotal for orders imported via a plugin.
It looked like the default payment method for this was “check” and I verified with the plugin developer that the payment method was WooCommerce’s default “check.” I have that enabled as a payment method but do not use it for anything else. But it does not add any fees to these order based on the payment method. Other fees based on payment method work fine.