If by flat head you mean “-“ shape then the main reason is that if you don’t have the drill bit centre plain in the exact same plain as the screws then it’s a n

If by flat head you mean “-“ shape then the main reason is that if you don’t have the drill bit centre plain in the exact same plain as the screws then it’s a nightmare to remove. For metal of pre threaded holes this isn’t an issue but drilling into wood where even with a pilot hole you can be a few degrees of perpendicular to the surface flat heads are significantly slower to work with.