The Transbay Joint Powers Authority is not all that independent. Its board includes the head of San Francisco MTA (an appointee of Mayor Gavin Newsom), a representative of Mayor Gavin Newsom, an elected AC Transit (Oakland-Berkeley-East Bay) board member, a member of the Caltrain board, and Chris Daly, one of the left-wing members of the San Francisco Board of Supervisors.

What this means in practice is that the TJPA board is basically run by elected officials from SF. San Francisco voters have on several occasions approved the Transbay Terminal project and the downtown extension and have created some pools money to do this.

The California High Speed Rail Authority Board is more independent, for whatever value it has (more on this later). Its members are appointed by Governor Arnold Schwarzenegger and confirmed by the state legislature, but the governor has taken a less overt role in leading the board than Newsom has with the TJPA.

These quasi-independent board have a weakness in that they're not clearly personal domains of a powerful figure (whether that's the mayor of San Francisco or the governor of California). So it's not quite as simple as Gavin or Arnold or anyone else coming in and saying "get this done".

In practice the TBT is San Francisco's project and Gavin Newsom has in fact asserted a very strong role in ensuring it gets built. Newsom has not had a big place in the HSR project. If he somehow gets elected governor next year (he is a candidate but I do not expect him to win) then he would be in a commanding position to resolve this dispute by potentially appointing new CHSRA members.

There's also a proposal to create a "Department of Railroads" within state government, to house all rail programs and regulation within that instead of under the Department of Transportation. That would include moving the CHSRA into a Department of Rail. I'm not sure that's the best idea, but it is out there.

There is no opposition to the TBT project. The CHSRA is making this weird "omg we need a second level to the trainbox" argument without really explaining why, at a late date, and the SF political leadership is trying to figure out wtf this is about.

And the world will live as one