I think you're asking why don't you retract the flaps at a lower altitude? Remember distance is your friend for noise reduction. In order to retract the flaps you have to lower the nose to increase your speed and this lowers your climb gradient. You're only worried about the first 3000 feet of climb. The tech people have figured out you'll spend more time down low retracting the flaps even if you will have a better climb once they're up.