There are several things to consider (based on the handful of kids I know who have taken a year abroad in high school. )
First, if you go to a local high school, it will help you learn Japanese. It will not help you learn chemistry or history or whatever else because your language proficiency will be an impediment to that. So you need to be sure you have met all your requirements-- not just what uour US high school wants but also what colleges want – outside that experience. A friend’s kid got majorly messed up by assuming her junior year in Europe would basically be high school and language immersion. It was really only the latter in large part. Her college admissions process was challenging at best and it also made her feel, once at college, that she was missing enough in her foundation that certain as academic paths were not open to her. Granted, that’s one person but it does shed light on what could go wrong. (I realize your plan is to do it all in 3 years before you go.)
You would be well advised to have your standardized testing done before you go if you are going senior year. No need to add the stress of getting to a test center and preparing when your head is someplace else.
If you want to do this because of the experience, I really think the gap year option is the best. If you think it will help you in college admissions, I would see if you can do your junior year twice - once at home and once in Japan. That way, it’ll be part of your application without all the challenges of being a year away from high school requirements.
If you do it your way, you will still have college options so if you are willing to be a little more fatalistic about it – some colleges will like what you’ve done and others won’t and the ones that do better mirror your priorities and sensibilities – go for it. If you are truly worried about making the best case for a certain set of schools, I would play it safe and make it an extra year of high school.