I think the study linked above suffers from the same problems as Rick's fare maps. For Germany, at least, they assume full walk-up ticket prices, when considerable discounts are available for advance purchase (Spar Preis), slightly slower trains (IC vs ICE), and several people traveling together (Länder-Tickets).
According to the study, the three trips they show, Berlin to Cologne, Munich to Stuttgart, and Cologne to Duisburg total 907 km. The walk-up ticket prices from German Rail add up to 181 euro. That's 20 euro cent per km. But using SparPreis ticket prices, the total fare is 72,70 euro, or 8 euro cent/km. Similarly, a trip I took in 2017, from St Goar to the Ost Allgäu (SparPreis) to Lindau (Regional pass) to Rothenburg (Bayern-Ticket) cost me 138,40 euro for two people, or 8.8 euro cent/km/pers. Walk up tickets for the same trip would have been 21.7 euro cent/km. So the prices in the study are more than twice what one can get taking advantage of discounted fares.
Full fare is only paid by people who don't, or can't, plan ahead, like businessmen traveling at the last minute on the company's dime, but then that comes out of a company's budget, not the median disposable income for a person. It's just like businessmen paying full price for last-minute airline tickets in the US. The study is irrelevant for American tourists planning months in advance, but then it wasn't meant to apply to us.