The most expensive thing would be hotels, as in most of Japan they charge by person, not room. Young children excluded I think most places.
Food can be quite cheap, or expensive - huge range of options. Japan is overall on the expensive side, but has been living with stag-flation for a long time.
Transportation...I'd strongly recommend public. Tourists can get a JR Pass that they can use on any line -
fantastic deal
https://japanrailpass.net/en/
If you want to drive (recommend outside Tokyo only) rentals are pretty reasonable, but gas is expensive.
The big thing for me when I rented a car here for driving in Hokkaido was how clean and perfect it was compared to my rental on Hawaii visits
I think over all food and rooms felt similar to when I stayed in Rome and Firenze.
At least I don't recall feeling Italy was super-cheap, which means there wasn't a remarkable gap for me.