I don't think your sources support your claim -- but it's complicated. The first link:
https://theicct.org/planes-trains-and-automobiles-counting-c... has a graph showing that bus achieves ~150 passenger miles / gallon gasoline equivalent, compared to amtrack, plane, and car all at ~50 +/- 10 miles / gallon gasoline equivalent. Bus is 3 times more efficient than the average car by that measure -- but it really depends what kind of bus loading they assumed. The second link:
https://www.cato.org/sites/cato.org/files/pubs/pdf/pa-615.pd... is mostly arguing that trains should not be built _in the US_ for environmental/efficiency reasons. One strand of the argument is that building rail is less flexible and takes away ridership from the more efficient bus mode. I think this is the passage you were trying to quote:
> Two commuter-rail systems —New Jersey Transit and the Northern Indiana Commuter District—are the only transit systems that use less energy per passenger mile than a Toyota Prius. All other commuter-rail lines, except for the SEPTA system in Philadelphia, use less energy than the average passenger auto.
Quite the contradiction to "none are even close to being as efficient as driving a Prius".