Yes, it is not about politeness, it is about conflict. In France, being frank is a quality, in Japan it is a mark of immaturity. Grown-ups are supposed to communicate their opinions implicitly.

I stopped finding it "interesting and different" when I realized that it led to a LOT of miscommunications even among Japaneses and could end up ruin lives because of the unwillingness to point out even minor things.

Happy to hear this is mostly a Tokyo thing (though it does extend to my coutryside in the Chiba peninsula)