Transport time calculations using the max speed of >500km/h are misleading. I doubt that all passengers want to travel from one end to the opposite end. You might need to travel any partial distance to visit relatives, concerts, doctors etc. So you need to add many train stations (6 min walking distance: one per kilometer? Probably not, more about 10-20 stations over the total distance), or add hub and spoke design with other (slower) means of transportation and introducing inconvenience of changing transport 2-3 times, or multiple lines in parallel covering smaller parts.

There were concepts many years ago to have commuter capsules accelerating and dock to longer high speed trains, to avoid the slow-down of stops at stations.

I like the idea of using only 5% of the real estate and preserve 95% theoretically untouched - but the gigantic building will certainly change the surrounding environment by blocking air flow, reflecting sun to south, adding shadow to the north, etc. and you need to add lots of solar or wind farms, probably outside the actual building.

This gigantomanic plan is more an expression of prestige, non-democratic power, and an excellent way to totally police the people inside. Another useless waste of money, energy, building material, nature, probably human live of slave labor.

A useful project would need to include all stakeholders in the design phase, including a democratic process to define targets, outcomes, financing etc.