Would a codeshare passenger face more restrictions vs a passenger booking directly on JAL? Pretty sure when I booked JL3/JL4 earlier this year in J with no status (through Chase UR), I had the ability to choose at least some window seats. Maybe they were the ones open to non-status pax.
I did a dummy booking on JAL and indeed I could pick window seats. I think the first two rows were blocked though. All window seats blocked to codeshare bookings though.