What aircraft type are you talking about?
The only time I recall having to inhibit the Flap Inhibit Switch was when a new runway was constructed and the Terrain database was not yet amended, thus to allow a flight near the ground to be permitted approaching the *new* runway.
An EGPWS Terrain database allows you to fly near a runway (approach area) lower then it does outside this area. Thus inhibiting the Flap Inhibit in this case allows an approach without the alerts sounding when approaching short finals. There should be no other reason to use this switch in normal operations.
The logical step for operators who operate into arenas where such action is required for the above reason is to update their EGPWS database.