You are able to check-in or check-out anytime during the shop's open day and hours. There is no need to contact support.
Even if you check out early, your payment for the original reservation will stay the same and the difference will not be refunded.
You will not be able to check-out more than 1 day early if you have made a consecutive reservation inside Tokyo JR Station, as your luggage is being stored in a separate warehouse. Please contact support if you need to do so in this case.