For most travelers, it is the only document you show at the border.
> Countries deny people with valid passports from entering all the time. For example, if they don't have the proper vaccines.
In theory, yes. In practice, no.
I have never once seen a Japanese traveler required to produce any medical paperwork along with their passport (and I have flown a lot between both countries).
Could a traveler from Japan in theory be stopped at the border for a lack of vaccination? Probably. How often does that happen? Effectively never.