I don't know about elsewhere, but some of this might not work anymore. As mentioned JR sets a limit of about 2 or so hours.

For example if you use your say suica commuter pass to enter Yokohama and exit using a another ticket or pass at another location (so your suica commuter pass never shows an exit) then you try to return to your ORIGIN station (eg Yokohama) after a few hours the alarms will sound and the gates will shut. My friend tried doing this, using their pass to enter their home station, then they went to another station exiting using another ticket, but on their return about 3 hours later, while trying to exit their origin station the alarm sounded, and since my friend isn't a good liar almost got into big trouble, they just paid 2x the price of the fare.

Any case it has happened to me as well but I never left the system, got on one day to ride trains for about 6 hours, tried to exit again at my home station and got all the buzzes and whistles.

But as for the Tokyo Metro fare, yes, it just assumes you will take the most direct route and charges it. Other times there are special fare routes where it will be cheaper or more expensive then normal depending on competition with other railway companies. For example, JR has special pricing between Shinagawa and Yokohama (if I recall) because Keikyu trains also run that route.