The use case is routine. A lot of people, most of the time, do indeed want to "take the train". Heroic feats of real-time planning have their place, and it's great to have tools that help you with that, but routine can be covered with much simpler tools just as well.
Even in the Tokyo scenario you gave (which is fascinating -- thank you!) Google gives 30-40 min. for most public transit options, so for rough planning they're all equivalent. Taxi is faster, and bicycle is almost at par.