> In Japan, each train line is a different and separate fare.

Each system, not each line. It's easy to travel without crossing into different systems most of the time. Also it doesn't even matter too much because you pay by distance, and all you do when going between systems is tap at the gate, so a route from X->Y via one system or via two different systems does not usually change the price that much.

Also the time of the last train really depends. On the Yamanote line the last train is 1:20 and the first is 4:30, so that's only a three hour window, they sure aren't doing huge amounts of maintenance in that.