The article takes into consideration quite a number of considerations, and concludes that - for the very specific journey that the authors took and were analyzing - their train journey actually “cost” over 366kg more CO2 emissions per person than a plane would have been. That said, it did note that

Thanks to the absence of jet contrails and their associated water vapor emissions – a major component of non-CO2 radiative forcing – we estimate that our total climate impact was 37% less than if we had flown, even if our CO2 emissions were 28% higher.

Regarding making the same journey by car, they say:

Carpooling from Boston, whether in an internal combustion gas engine or an electric vehicle, emerged as the least emission-intensive travel option for this journey. Additionally, driving could be a faster alternative to Amtrak if the team rotated driving responsibilities and continued without extended breaks. [Snipping a bunch of their considerations here, but feel free to read the article.] Consequently, emissions for each traveler in the electric vehicle stand at just over 18% of the equivalent emissions from a direct flight and 25% of the emissions from the predominantly diesel-powered train journey.