For land rights issues it is easy enough to create stations that are sufficiently distanced from the city centers but close enough to tap into local Bus/Uber-ish/car rental options. Most Californian metropolis' have an area distanced enough but accessible where land is still relatively cheap, the exception being LA which has sprawled into Orange County and completely enveloped other regions.

However going through mountain in an environmentally conscious way gets radically expensive in very short order. Additionally this style of construction tends to have its own legally contentious issues. (Dam construction for water management being comparative)