Your passport could very well be checked if you're crossing from Austria to Germany. I had such an experience in Freilassing in June, the train had stopped, I had dozed off. The Bavarian police appeared, asked me for my Passport in German, surprisingly. (the 2nd time that happened when crossing the Salzburg-Munich corridor.) The first time was in 2015.
No scanning but they will flip through the pages, it isn't really a cursory glance either. They're looking for more than merely your name and photo. (I didn't know that in 2015, this time I was prepared to deal with them as I knew what they were after). The one guy asking the questions as he was flipping through the pages of my US passport asked me if I spoke English (which really ticked me off). I just shot back the answer at him.
I noticed whenever I made a border crossing between Germany and Austria at another point / location other than the Munich-Salzburg corridor I never encountered a passport check, day or night.