It would not surprise me if they discovered an even earlier pre-Christian site below that. If a site isn't established because it commemerates an event at that site then it is often built on top on someone else's Holy Site. It is either done to "wipe out" the heathen influences or because the locals already percieved the spot as "holy".

In this case it may have been selected for its seclusion and then once deemed "holy" subsequent churches were built over it.

 

Exactly. Another is in Assisi. The was a huge temple to Minerva there and in the early Christian period it was "renovated" to become a Christian Church. Early cultic symbols still survive. The Cathedral in Mexico City was built over Aztec holy sites. And of course as you rightly point out, the "Dome of the Rock" in Jerusalem is built over the site of the Solomonic and Herodian temples.

I am not aware if early Christains ever built a worship space on the temple mound that the Moslems over built. I don't remember reading about any and can't find a reference to one. That would be an odd omission if it didn't happen.

Oh well, off to lead my own worship services.