As far as I can see USB_USBTask() manages the control endpoint when it is not handled via interrupts. However if you do use INTERRUPT_CONTROL_ENDPOINT, it is not required and should be removed.
You could then remove the function completely in the lufa source via #ifdef INTERRUPT_CONTROL_ENDPOINT which will result in a compile error. Most users will not know what to do then, why the symbol is missing.
As an alternative you can declare the function as depreciated with a custom text, warning that it is useless when INTERRUPT_CONTROL_ENDPOINT was used.
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