Agreed. The cost for underwater tunnels will be much higher - especially initially. Let's say they are 100X higher cost at $100mil/mile - that is still 1/30th the cost of a current tunnel in San Francisco at $3bil/mile. But the Boring Company is already designing for air tight tunnels: 'vacuum-sealed'.
"TBC’s current tunnels are designed and built in preparation for their eventual transition to Hyperloop."
"Hyperloop is an ultra-high-speed underground public transportation system in which passengers are transported at 600+ mph within a vacuum-sealed tunnel. Whereas Loop is used for shorter intra-city routes, Hyperloop will be used for longer inter-city routes."
"TBC’s current tunnels are designed and built in preparation for their eventual transition to Hyperloop."
"Hyperloop is an ultra-high-speed underground public transportation system in which passengers are transported at 600+ mph within a vacuum-sealed tunnel. Whereas Loop is used for shorter intra-city routes, Hyperloop will be used for longer inter-city routes."
https://www.boringcompany.com/faq