I think the rules are pretty clear and the flight is not eligible to earn Flying Blue miles and XP.
Earn Miles and gain XP on flights marketed as Japan Airlines (JL), Japan Trans Ocean (NU) AND operated by Japan Airlines, Air France, J-Air, Japan Air Commuter or Hokkaido
Alaska Airlines is not a valid operator for JL coded flights that earn miles and XP - so no mileage can be earned.
It is the same with what has happened with Etihad - you earned miles on a Etihad flight under Air France flight number - but not a single mile for a flight on Etihad under an Alitalia flight number - simply because the AZ marketed flight was not operated by an official parter airline of Flying Blue.