One of the rooms is intended for a solo traveler. Asaba doesn't seem to accept this - I understand Ryokan typically charge by person and not by room.. We're fine to pay for two people, though, with single occupancy. Are Ryokans typically accepting?
Yes, I do it all the time. Book for two, pay for two, arrive as one. I've done it twice at Asaba, in fact.
Some ryokans charge a single supplement (rather than requiring a minimum two person $$ stay), although I haven't kept tabs on which ones have such policies.
Worst case - if you encounter a situation where they get nosy about your intention, you can simply tell them that the second traveler fell ill and couldn't make it.