I'm sure this hotel's check in process and rules makes sense to the people who created them, but, at least as a foreigner, I have to say they make no sense and lead to a poor check-in experience and bad first impression.
Apparently there is some membership you can buy for ¥1500 that gives you a rebate on reservations made directly with the hotel and gives you priority check in at 3pm instead of their usual 4pm. 4pm is a bit late, but I understand giving your own members a preference and priority. Fine. Note that I had to research and figure this out on my own, after the fact, because none of this was communicated to me directly.
This makes no sense, however, when someone shows up at 3:20, exhausted after a 15 hour flight from followed by 4 hours on the train, and despite having a room ready and sitting empty, you force them to sit and wait a half hour until exactly 4pm rolls around. I pre-paid my hotel so I wouldn't get any discount from the membership anyway, so what this policy (or, more precisely, the crazy implementation of it where you make people sit and wait needlessly) effectively does is punish tourists who are either first trying out your hotel or someone visiting only one. This leaves a poor first impression and discourages me from returning.
Also, if you are going to have this policy and enforce it so blindly, you need to do a better job of informing and accommodating guess. Don't just tell me to sit for an undetermined amount of time.