Oh yeah, as is it works off a hook on a per-module basis. So, any module implementing the hook will be listed in the settings menu as a recurring fee handler. You just can't specify a different handler depending on payment method right now. If you had a custom module and implemented your own hook_recurring_fee(), you could have that check $order->payment_method and kick out to a different charge function accordingly. So... it's possible, just roundabout right now.