Not just for security - generally speaking if you have high speed rail infrastructure connected to a good and fast public transport grid, there's genuinely no reason to build a huge city.

High density housing is very slow to traverse and getting from point A to B in a big city might take more time than getting on a train that takes you to another city 200km away in 30 min. In a traffic jam, you'll be lucky to do 5km in the same time.

You have it backwards. Passenger railways only make sense when they connect large population centers. Public transport networks outside of urban areas barely exist.