Directly above the passage quoted in OP is this:

When I was young, there were many attempts by religious people to "reconcile" science and religion. For example, each of the six days of creation can be viewed as representing a different geological era. There was - and perhaps still is - a view that science contradicts religion, that one has to reconcile them. It is apologetic, and I don't buy it.

He is swallowing the bullet on separate magisteria, here.