On one hand, as you mention, we experienced lots of acts of politeness, as I would put it, e.g., being helped to find some location as in your example, being helped to understand some menu dishes when I couldn't decipher them (I had at most intermediate level of Japanese), being bowed to upon entering hotels, ryokans, etc.
On the other hand, we also experienced straight up nasty behaviour, e.g., someone standing up and leaving the train wagon when we sat next to him (and then reentering through the next door and sitting far away from us), being forbidden from entering a bar because of being foreigners (despite the fact I can speak Japanese, not great admittedly, but more than sufficient to order, pay, etc.).
When talking with people from my country settled there the common negative theme is "you'll never be accepted/treated as one of them".