No, that is not the case with online check-in of JL operated AA flight number, unless thing has changed in past two months. I have flown JL operated AA flight number more than few times. I assume this is AA issued ticket.

For online check-in you have to start from AA website. JL check-in starts 72 hrs. before the departure (although issuing of boarding pass does not start till 24 hrs. before the departure). You start from AA website with your reservation and 72 hrs. before the departure “Check-In” function will appear on your reservation.

AA website will then redirect you to JL website and you will able to do seat selection and complete online check-in, although you will not able to print the boarding pass till 24 hrs. before the departure.

If you go directly to JL website with JL confirmation number and start online check-in from JL website, then will tell you that unable to check-in.

It will be nice if the procedure is same between any alliance partners, but that is not the case at this moment. From my experience AA-BA situation AA can online check-in for BA flights. AA-AY, AA could not print boarding pass but from AY website I could, at airport AA agent could print AY boarding pass.

AA-JL situation I can see JL reservation at JL website using JL confirmation number, but on AA-CX situation I cannot see CX reservation at CX website using CX confirmation number, but if I call CX an agent can see my reservation using CX confirmation number.

Looks like each alliance partner is different and have to figure out case by case.