It doesn't really matter; travelling together doesn't mean you'll be guaranteed seats together, but if you are in J you get seat selection included so can do that as soon as you book.

Just means if there are changes to the flight you'll each get told separately.

If you were in Y it could be an issue because Y is overbooked so one of you could be bumped off the flight (or upgraded) without the other. J isn't overbooked (as far as I know) so no danger there, and you can't upgrade either.

I've booked flights separately from someone I travel with for years (mainly in Y), never had any issues.

Of course there's no guarantee the 2nd seat will go up by $1000.