When including an image in an answer to this question: Was New Horizons launched on a copper rocket? I noticed that for the larger diameter fairings (Atlas 501 and up) the Centaur upper stage is submerged in the fairing.

Why?

This makes the fairing a lot longer than it would be if it was mounted only to the top of the Centaur as it is on the smaller models.

The answers to this question Why does Atlas V have so many different types of payload fairings? don't address this issue.