[w0de0]

How can this entire thing be written - including the observation that most entrances are “in or near” Christian churches - without even mentioning the extraordinarily obvious conclusion of forced or voluntary anchorites?

There is a deep tradition of chthonic ascetic monasticism in Christianity. Many, many Churches from this same period have attached anchorite cells.

It is easy to imagine similar cells/tunnels being used, unremarked, by choice or coercion.