On the day it would be up to the local JAL staff, in the first instance, to decide what to do with you when you turn up very late for your flight. Now, to paint broad brush strokes of the Japanese culture, there will be both a tendency to follow rules strictly, and a tendency to try help you within the limits of the job role of the person you are talking to (especially if you ask very politely). It may be that, within the rules, a way can be found to help you, but that is hard to predict ahead of time here and now. So it's very hard to predict whether you will be told, politely, that they can help you for some reasonable change fee or even for free or whether you will be told, politely, that there is nothing they can do and the cost of a new ticket is ¥many. I have had both, more help than not, but both have happened to me.

Hence the need for your own contingency, in some combination of time, funds, or insurance.

I tend to think that I could find something interesting to do in most places in Japan for a day even outside my primary destination; even looking at local parks, shrines, walking the neighbourhood, finding the local food speciality and consuming some of it, and so on. So I would be inclined to add on extra time in case of schedule irregularity and then make something good of it.