All this work is impressive, but I'd rather have better trains
As someone who lives in the Bay Area we already have trains, and they're literally past the point of bankruptcy because they (1) don't actually charge enough maintain the variable cost of operations, (2) don't actually make people pay at all, and (3) don't actually enforce any quality of life concerns short of breaking up literal fights. All of this creates negative synergies that pushes a huge, mostly silent segment…
1) is a bit simplistic though. I don't know of any European system that would cover even operating costs out of fare/commercial revenue. Potentially the London Underground - but not London buses. UK National Rail had higher success rates
The better way to look at it imo is looking at the economic loss as well of congestion/abandoned commutes. To do a ridiculous hypothetical, London would collapse entirely if it didn't have transit. Perhaps 30-40% of inner london could commute by car (or walk/bike), so the economic benefit of that variable transit cost is in the hundreds of billions a year (compared to a small subsidy).
It's not the same in SFBA so I guess it's far easier to just "write off" transit like that, it is theoretically possible (though you'd probably get some quite extreme additional congestion on the freeways as even that small % moving to cars would have an outsized impact on additional congestion).