For some parts that are supposed to be curved (like those outboard seat ribs), you don't flute to make them flat, but you do have to flute them to get the proper curve. In these cases, flute until the holes line-up.
I remember initially looking at those ribs being very confused because they come curved the opposite way. Be careful to flute incrementally though... very light pressure on the first pass. It really doesn't take much to put a large curve in.