The bonded or punched as you call it is manufactured so that it is more durable. Typically you can quilt further apart with these.
When you read labels, they talk about loft, distance between quilting, content, shrinkage.
Like sharon said, a lot depends on the look you are going for. Also, the closer you have to quilt, the drape changes and the quilt can become "stiffer" feeling. That is another consideration.