Give people a choice between two houses, one that will last their full lifetime and then some, and another that costs double and that will last 500 years, almost everyone is rationally going to pick the former option. There simply isn't much present-day utility in over-building to such an extent.
And keep in mind, there are plenty of all-stone buildings that have collapsed from earthquakes and other natural disasters, killing many people, e.g. https://en.wikipedia.org/wiki/August_2016_Central_Italy_eart... . A lot of construction methodologies that last 500 years only do so in some environments. Against a lot of common risks, a modern building constructed of dimensional lumber is better.
And anyway, I still think the better comparison is between the average building in different time periods, not the best buildings (which are basically just outliers).
The overall idea that I'm trying to get across is that the best homes of today are not nearly as durable as the best homes of 500 years ago. The historical home would have had likely had stone walls if the owner could afford it, and a heavy timber-framed roof with lead or zinc overlaid for protection from the elements - exactly like Notre Dame, in fact. A modern home of the same cost (i.e., belonging to a person of equivalent economic class) is going to be much more comfortable but is much less likely to stand the test of time - at least, unless it substantial ongoing maintenance.
To put it another way, after a hundred years of abandonment, the historical home would likely still be standing. Barring extreme weather, the roof would likely be still in place. A modern home however would decay much more quickly, because of the assumptions that we make today about the availability of quality materials for repair and maintenance - and yes, because the materials to which we have access today allow architectural styles that were previously impossible, like huge bay windows.