Married segment logic (rules on which combinations of flights are allowed and their pricing, which is what is happening here), can certainly apply to award as well as paid tickets depending on the IT of the airline. I don't know exactly how Alaska does it and how strictly it follows JAL's rules, but if Alaska is asking JAL "is there award space on OKD-HKD-HND?" and JAL replies "no", then there's your answer.
For comparison, American also seems to follow JAL's rules and won't return any options for OKD-HKD-HND. Delta is relatively strict about married segment logic for awards. United less so, although it could be either United or ANA allowing unusual combinations for their domestic awards.
The 65k figure is likely a bug since there's no obvious reason it should price that high. But it's also likely that the "correct" answer is that it shouldn't be showing up at all if JAL is saying there are no seats on OKD-HKD-HND, and it may give you an error if you actually try to go through with booking it.
I see. I agree that this is the most likely explanation, it just irks me because I know there are exceptions, intentional or not. I actually just flew one the other day where I was able to have it route me CTS-HND-ITM instead of simply CTS-ITM so I got to stay in Tokyo for a while
I wonder if this would change with multi partner awards coming in soon. My intuition says yes, but not sure.