I guess a lesson learned. Hopefully, the 2nd guest surcharge was minor. Anyway, you received the reply that I would have expected you to receive from most hotels (why refund anything that you don't have to refund - it doesn't make commercially sense).
Japan is one of the markets where the rate for 2 guests are usually higher than a single occupancy rate. As I almost always book single occupancy rooms, I have nothing against this (actually I prefer it, assuming that this practice in general leads to lower rates for single occupancy rooms).