I just reread
They Have their Exists by Airey Neave. In his account of his 1942 escape from a POW camp at Colditz Castle, he mentions he traveled by train from Leipzig to Ulm, which required a transfer in Regensburg. He and his companion shared a compartment with an SS officer who was heading for Munich. So it seems that the train from Leipzig to Munich passed through Regensburg. I checked the available service using Google Maps (which might not be 100% complete), and it seems that if you travel from Leipzig to Ulm today, you don't pass through Regensburg, and the only way to do it is to travel all the way to Munich and change trains there. It has occurred to me that one of the reasons the rail network in this part of Germany might not be as complete as it used to be is that the route from Leipzig crosses the former Iron Curtain, and some through tracks may have been removed during the Cold War. From Ulm, they wanted to get to Singen, but this town was so close to the border that it attracted the attention of the authorities, so that had to sneak out of town before they could be arrested and took a train from Laupheim (an outlying town) to Stockach via Pfullendorf. According to Google Maps, you can't do that today. You can take a train from Ulm (or Lauphiem) to Friedrichshafen, change to another train and ride to Ludwigshafen where you have to change for a bus to Stockach.
Later on, Neave and his companion successfully cross the border into Switzerland, where they end up in a town called Ramsen, which is in a small part of Switzerland that protrudes into German territory. According to his account, the Swiss police took them on a train ride to a larger town, Schaffhausen, which involved the Swiss train crossing back into a salient of German territory for a short while, which freaked out Neave. I studied the map carefully, but it seems that there is now no train service to Ramsen, and I couldn't find any local rail routes in the area that cross into German and go back into Switzerland.
As for the rest of their journey, they were smuggled out of Switzerland through Vicy France and into Spain. There wasn't as much detail about the train rides they took, but they rode from Annecy to Marseilles, form Marseilles to Toulouse, from Toulouse to Perpignan, where they were smuggled by foot across the Pyrenees, and then a train from an unspecified Spanish border town into Barcelona. From their they were transferred by car and charter bus to Gibraltar, where they took a troopship back to England.
So it is true that you can't ride trains in Europe now that you could 80 years ago.