Perhaps the website can't deal with the codeshare, the website is fairly clear that both AA or JAL would earn on I class at 125%, although it does say "international only" I am hope this would be fine..
https://www.asiamiles.com/en/earn-mi...japan-airlines

The website calculator only offers First class to earn miles though for JAL as there isn't a business class cabin, so perhaps this is the confusion, not knowing if you will be put into domestic first?... https://www.cathaypacific.com/acc/en...sia-miles.html
(If you choose American Airlines it does show business class mile earning)