Part of the future will be an underground high-speed rail system. This will be important, but a very expensive project. Building an underground hyper-loop system will cost millions of dollars per km. This will be a big investment if the nation is about the same size as an average size nation. With that in mind, the goal will be to move a part of the system underground. It might make more sense to have both types of lines running underground, but this will cost problems that might not otherwise be apparent.
What will likely happen will be to move passenger trains to remain above ground, on newly constructed high-speed rail. This will allow the passenger to have access to the internet, and be able to connect to family and friends while riding. Even if high-speed rail cuts an 9 hour trip in half, this is 4½ hours travel. People might need to get work done, and be able to communicate whether using the train’s wifi network, or carrying their own data service. This will be a logistical nightmare to do this underground on a hyper-loop system that would somehow need constant connection for services. With that said, it is better to push the passenger rail network to remain above ground.
However, freight does not need a connection to the internet. Freight is non-living and won’t complain they can’t connect to the internet. With that said, freight can run 24/7 and not interfere or be interfered with passenger trains. Freight trains will be loaded and unloaded above ground. The train will then go underground by track to the high-speed rail system. The train will then travel underground until it is about to reach its destination. The train will make their way above ground to get unloaded. The train will also get loaded if there are shipping container that need to be loaded, and the train will continue on their trip. To help cover the cost of operations, the freight company will pay a rail fee based on the km traveled, and docking/undocking fees. The travel fee will be to maintain the underground system, and the docking fees will be to pay the dock workers. And since there are dedicated lines for both passenger and freight, both systems can run 24/7 without any issue based on demand of the system.