That really only applies to bottling from a keg. You pour the pre-carbed beer slowly into the bottle, and then apply the cap on the foam so that you are not leaving oxygen in the dead space.
You will not have carbed beer when bottling from a primary or secondary, so there will be no foam.
“Here's to a long life, and a merry one;
a quick death, and an easy one;
a pretty girl, and an honest one;
a cold beer - and another one!”