If you have GPS and a good terrain database it would be possible to develop a system that knows the aircraft is low over water with flaps down or low over land with flaps down. The system would then know if wheel should be up or down and could alert for an incorrect configuration.
I'm actually surprised no one has developed such a system and perhaps they have. Perhaps they were discouraged by the problem of making low approaches over land surrounding the intended water surface.
Accident history shows pilots are adept at ignoring loud and prominent audio alerting so not convinced that either the simple system you proposed , or the more complex one I suggested, would guarantee you will never land an amphip with the wrong gear configuration.
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