Regarding trains, I don't think that's really accurate. Yes, a train that's completely full gets excellent effective mileage per passenger for that trip. But how often are they anywhere near full? In reality, trains and buses have to make a huge number of runs either completely or virtually empty in order to have a regular enough schedule for anybody to be willing to depend on them. We need to know the effective fuel consumption of all runs actually made per total actual passenger-miles transported over the course of at least a week, maybe more like a month.

And that's before we account for any additional trips needed for personnel movements, car and track servicing, and other such things.

Those numbers are from Bart and Caltrain's operating reports.

The Bart number may have been during peak only so fair point there, I can certainly look for the systemwide average. [1]

The Caltrain number is average over FY2016-2018, from their sustainability report page 5. [2] They completed roughly 436M passenger-miles per year, and consumed roughly 4.4M gallons of diesel. Clocks in around 100 passenger-miles per gallon. I'm sure its worse now with the COVID numbers. I think it's a fair ballpark point of comparison though, and you can consider the Bart number an upper limit.

You're of course right its a function of ridership. An average freight train gets over 400 miles per gallon per ton of cargo.

[1] https://www.bart.gov/sites/default/files/docs/GreenSheet.pdf

[2] https://www.caltrain.com/about-caltrain/sustainability

No, what matters is the marginal additional emissions of a passenger choosing to ride the train. An empty train is going from A-B regardless.