I think it comes down to new non-functional requirements: safety, environmental concerns, accessibility, liability protection, etc. With these requirements, Paris or London or New York would have never had a subway system in the late 1800's or early 1900's. By now though, all these systems have been maintained and modified to comply to the new non-functional requirements over time.
So if you added the accumulated cost of running a subway system today, while adding all the maintenance costs over time, it might be the case that the cost of building the same thing from scratch would be cheaper, but unfortunately without the benefit of having passengers enjoy it (and pay for it) for over 100 years (thus partially subsidizing the maintenance costs).
So you could even consider something as rigid as a subway system built in an "agile" way, with a quick and literally dirty MVP out of the way early, and additional non-functional requirements added over the course of decades. It's just that those requirements weren't known or wanted initially.
Now would it be ok to do the same now? Have a subway system in a city that needs it, but without bathrooms in stations, with no pollution requirements initially, not accessible to the disabled, (name your other requirements not necessary for a MVP), but with the benefit that at least it exists now, it can be subsidized by passengers that are willing to use it, so that over time those other requirements are met. Better have them later than never.