SANDAG apparently thinks they will spend about $4B for r/w & construction, but there seems to be a lot more than just a basic hole in the ground going on. As there should be, with a comprehensive realignment. Compare a complicated job in an urban setting to one that had complications but not urban ones, and factor in a 30 year inflation of construction cost and other requirements, and what SANDAG expects is probably reasonable. SANDAG has done a pretty good job so far at properly estimating (and delivering) their railroad (and highway) work so I'd go with what they have. You can gripe about how everything costs too much in the US and CA it but that's what it is.

In reality, no two tunnel jobs are the same, and it's impossible to make a simple comparison especially widely separated in time, purpose, and environment. In the Del Mar case, I like the concept of the shortest, fast alternative, but whether that ends up chosen will depend on a fairly extensive study & design process (for which they're planning a lot of money, too, and rightly so). It's potentially a 3-4 mile tunnel, which longer than average for CA rail lines outside of some subways.

They're rightly concerned about where they'll find the money, especially in the current political environment, but that's what MPOs' basic job is: finding the money. Assuming the feds' money doesn't go totally away, I'd rate the chances pretty good that SANDAG will have the project going about when they're currently planning it.