Going back to Ratatoskr, the sightseeing log for Tharl Oom Kash implies that was the site where Ratatoskr was slain, and her death is what produced the massive amount of crystallized aether in the area...much like how Tiamat's injured and bleeding presence is probably what is producing all the crystallized aether formations on that island where she is imprisoned.

As for the Cathedral, the Allagans had no religion at all, they only believed in technology. This is stated...hrm, somewhere! I think it was the description of a key item (there's a lot of interesting info on those for those of us who read em). So despite being called the Cathedral, I believe it is something else entirely for the Allagans and was simply called that (by whoever names the places on the map) because of its appearance.