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As with anything Ford, I'm sure it was a cost savings thing to eliminate the extra flange. They probably save at least one stamping procedure and 1/2¢ of steel per running board saving them $1 per running board. Could really add up in a two year production run.
I think Ford did everything because of a buck. I doubt thought of stupid ideas ever plays a major part in car design, just take a look at the new cars and trucks, they get uglier and stupider looking every year.
I would have to agree with Bob on this one. At this point it is all about cost effectiveness vs. the consumer appeal of their products. Just when I get use to one body style they make it uglier...