I'm a Tokyo local and yes, this is real. Even I find it uncomfortable. On the Yamanote Line during rush hour, trains come every 2-3 minutes and it can still look close to this.
That said, most people's daily commute isn't this extreme -- it depends heavily on the line and direction. The tradeoff most Tokyo residents accept is: 30 minutes of crowded train vs. hours stuck in traffic with nowhere to park.