I should think any rail tunnels or tubes in this area would face the same issue of hydraulic lift. I remember BART was worried about the Central Subway tunneling under the double-decker BART-Muni tube on Market St. at 4th St. for similar reasons and tapping into underground water sources.
All these issues, unknowns and liabilities should drive up the bids on any Caltrain to TBT DTX tunnels and associated station and storage structures. You have to wonder if it will be done at all. Kopp wanted to drop it entirely.