The ma’aleh in these Berditchever stories is that he was always able to point out the zechusim of Klal Yisroel, even when criticism seemed obvious and justified. I have heard a ton of these stories as I had a Rebbe who always foused his pre-Neilah speech on zechus K”Y.
The fact that he was able to see zechusim in everything does not mean that one should act like those characters in his stories. Obviously, davening at home beats davening on the train. They can use their time on the train to think about Hashem, just like in other m’koymos where davening/learning is inappropriate/assur (i.e. bathroom).