NEfan In my experience, Japanese hotels passionately follow the rules regarding maximum occupancy per room. Even as a Globalist I was not allow more than 3 individuals staying in a PH Tokyo Park Suite. As earlier suggested reach out beforehand and ask what they have to offer at this point in time.
Even if the area close to PH Tokyo is quiet, just a 10 minutes shuttle ride away is Shinjuku’s night life. Mercy me if I found this place two decades ago.
Concerning Kyoto, if possible give the city more time, just for the historical cultural experience. My latest stay at PH Kyoto was a life memory!
Happy travels!