I believe a number of happiness studies have found commute time negatively associated with happiness, but I don't have any references on hand, and if the ones you're seeing don't have that I'm surprised.

Indeed there are not studies linked to in the repository post.

Independend of that I'd read the advice more as the avoidance of useless time. Useless in the really useless sense of time where you can't read, think, talk or anything because you are busy looking for the next connection, switch trains, hurrying along and such. "daily reading hour" sounds like quite productive use of time but is only possible if there are longer stretches of uninterrupted commute.

If you dig down 3 links you find the Commuter's Paradox. I found this paper to use very reasonable controls and explain itself well. Sadly, it doesn't address your question about different modes of transportation.

Good question. I am not sure where I originally found the idea that shorter commutes make you happier, but I suspect it might have been an earlier version of this from 80000hours, which cites a couple of studies. Googling for pre-2013 media articles shows a lot of mentions of the idea as well.

The idea about a well optimized train or bus ride that Dr_Manhattan brought up also makes sense, if you live in an area with decent public transportation. It's the car drives that are a big time-killer, since you can't really turn your brain off while navigating through traffic, and traffic is usually more stressful at times you need to get to work.

There are a few productive things you can do during long drives though. For example, you can practice speeches, elevator pitches, songs, comedy bits, and so on without anyone hearing. That may not be quite as effective as interacting with another person on a bus/train, but the lack of an audience/consequences can make it easier to try out new things. Also, there's the option of consuming audio content (which you could also do with headphones on the bus or train).