My experience was a bit different. I declared at the kisok (case of wine), got the X, and the officer stamped and wrote something on my card. Customs guy looked at it puzzled, asked what I had, scratched his head, and said sorry, I had to to to Agriculture! The immigration guy thought I needed to go there for some reason. I go over to agriculture, they ask what I had, they scratched their head, mumbled something about the immigration guy not knowing what he was doing, stamped my card and I was out of there.
Anyhow, nobody wanted to ding me for extra duty - which they rarely ever do for this amount of overage.
It was the proper procedure, but the immigration guy got it all wrong.