I appreciate the very well thought out arguments in High Density Transit Oriented Development will not Reduce Greenhouse Gases. However, there are a couple of things that are glossed over.
One is the (hopefully) inevitable turn to electric cars and solar electric grid. When we think of Planning strategies, we must think 100 or more years into the future, because that is where the ultimate impact will be. The other item that is not addressed is the effects of these new ADU laws that require no lot coverage maximums.
As your data points out, Marin county sequesters 80K MTCO2e per year in its suburban areas, but this is only because of lot coverage restrictions. Without these restrictions, there would be almost no sequestration, because all trees and plant life would be gone from the suburban landscape.
One more thing that should be considered is the definition of mass transit. There are different forms of transit available, each with its own level of embodied energy. Light rail has a lower embodied energy (and uses less energy to run) than BART. There are additional, somewhat radical, low energy options, too, for consideration - aerial transit (like ski gondolas) and water taxis, perhaps even people powered ones!
Imagine if you could ride your bicycle into work in downtown Oakland but instead of riding over a bridge, you could hop on a boat, and pedal your way across the Bay. These ideas may seem far fetched but we need out of the box thinking.
We live near to an economic powerhouse of opportunity and it will continue to draw people from areas of disadvantage. People need to be housed but should not be housed at the expense of the environment. The only solution is to develop areas that are already environmentally "denuded", concentrating our cities at cores, with linkages that do not require people to sit in traffic jams when traveling from existing suburban, less intense areas of development.