Overhead (GPWS) is to reconfigure the ECAM landing memo and GPWS.
MCDU flaps3 is for the A/THR to know that Vapp is for F3 and to allow possible flight below F speed in managed speed. (GS mini will work regardless btw)
When landing with flap lever less than 3 (gpws flap mode off) don’t worry about changing the config in the MCDU as you will fly neither.