Lets assume it is some kind of maglev in a buried tunnel. How does this effect right-of-way? My understanding is the problem for building even a simple high speed train from LA to SF is principally NIMBYism and the resulting lawsuits . This causes costs to sky rocket as you get delays.
It will depend on the jurisdiction. In Australia, for example, what's under the ground generally belongs to the Crown in right of the particular State or Territory.
In general, however, almost any amount of haggling, land resumption / compulsory purchase and rezoning is cheaper than building tunnels.
We talk about disruptive startups. Bringing the cost of tunnels down by an order of magnitude would be fairly ... seismic.
(Unfortunately, the Earth is restless and heartless).
Keep in mind that America is famously horrible at doing public projects of this sort cost-effectively (e.g. the NYC 2nd ave subway is roughly four times more expensive per mile than similar projects in other countries, including very expensive countries like Japan). There are various reasons for this, but a lot of it seems to be dysfunctional bidding rules etc. that result in few bids and poor methods for choosing the winner.
Other countries manage to do similar projects for vastly lower costs, and it seems pretty likely that an intelligently run private project in the U.S. could also manage to do a good job of keeping costs down. [It's not just labor costs, etc either—total cost per mile is remarkably similar all over the world, both in cheap countries and expensive ones, except in the U.S.]
Limits are above and below ground. The FAA has a limit of 2000ft on structures. Beyond that you'll need to go to the mat to get special dispensation to go higher.
Depends if you have the mineral rights or not. You could argue that digging the tunnel is just a very inefficient way of mining your minerals (if you were a property owner, with mineral rights, wishing to stall the project). If you didn't own the mineral rights, there isn't much you could do if the tunnelers took care not to damage your (above ground) property.
Does digging a tunnel underground solve that ?