If the actual flap setting is not the same as that which we have programmed in the take-off performance page of the FMGS the config warning will be triggered.
On the A320, and assuming there hasn't been a software update I'm not aware of (which is always entirely possible), there will be no warning as long as the flaps are set to a takeoff setting. The system doesn't check that the actual flap setting tallies with that in the FMGC.