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He thinks it is pretty clear that these sequences have no major role in growth and development. "There has been a circular argument that if it's conserved it has activity."

Astonishing! So the question shifts from why is this region conserved to how is this region conserved.

Hypothesis: There exists a biochemical toolkit (see, e.g. The Wisdom of the Genes by Christopher Wills) for preserving specific regions of DNA, which prevents mutations from happening on those segments, rather than simply having death weed out changes to those segments. The map of where the toolkit is applied, however, is subject to change through evolution. Some changes to the map are weeded out through natural selection (i.e., changes that withdraw protection from certain vital segments), while others are not (i.e., changes that extend protection over unimportant segments).