Config Warning is actually a selectable option. We used to have a -500 from Maersk which could only do flaps 5 and 15, but not 1 and would set off the config warning at 1. However on our -300s we can use flaps 1.
Back when we were still owned by BA and used the performance data provided by them flaps 5 was standard, nowadays we use an EFB with boeing performance data and nearly allways use flaps 1, most of the time improved climb too, and that needed more adaption than flaps 1 vs flaps 5.