But the fact that even just a single rail car holds 360 commuters, equivalent to 180 cars or more on the highway changes the math completely.

Absolutely. The fact that 3 million people pass through Shinjuku station every day is a testament to that.

If all of those people lived in a city in the US it would be the country’s third largest, behind NY and LA.(If we’re going by the entire urban area instead just within city limits it would be the 20th, just ahead of the Baltimore-Columbia-Towson metropolitan statistical area.)

All in a single space that’s smaller than most highway interchanges.

And that’s not even using two-level train cars (which is where your figure for 360 people per train car comes from I think?).