Hi,
1. You can register a company in India or alternatively undertake a business from Japan only if you don't need physical presence in India. In that way, you don't need to pay taxes in India. If you open a company taxes will have to be paid in India and money should also be deposited in indian bank account.
2. You will have to take gst gst registration if you are opening a company in India. if you arr doing it from japan does not have india connection, you don't need gst registration. However, it is imperative yo understand overall mechanism and your preference.
3. It will be either in Company's account or your nre account.