As typically Japan is a very rules based culture and they will expect to, and respect, the rules that are detailed (whether or not you agree with a rule).

You can argue that this extra person charge isn't due in the USA very often, but in Japan if you see it on the rate details list, you should expect to see it on the bill. And removing it could be embarrassing for both parties (tantrums, arguments etc.). If you tried to hide the third adult in some way, would be even more potential for disagreement. The rooms themselves will likely be quite small too.

There are certainly rooms in Tokyo that are large enough for more people (The Prince Autograph comes to mind) and won't have the extra charge for some rooms, though often it seems based around extra children, for example Family hotels in Tokyo, Kyoto, Osaka.