Not everyone is standing on the train. The people who have the longest commutes usually also get on first, and thus have a seat. There are also express trains during rush hours... Do you have a source on the 50 minute average commute? 50 minutes on a non express train would be close to a last stop from the west side of Tokyo on one of the lines to the east side of Tokyo.

Here's an example involving one transfer and the last stop on one of the lines: https://www.google.com/maps/dir/Wako,+Saitama,+Japan/Tokyo+S... Currently it is 53 minutes.