Yep, different PNR's have never mattered in this regard, all you have to do is call AA. As long as you're in the same cabin, a companion on a different PNR is every bit as eligible to be seated next to you in MCE/preferred as a companion on the same PNR.

And I've never heard of any type of automated sweeps or anything like that. And even if that were the case, again a separate PNR companion is 100% eligible so it wouldn't/shouldn't matter.

The only issue I remember recently was the elite member who upgraded, then called AA to adjust his companion's MCE/preferred seats in coach. Once the elite member is seated in a different cabin than companions, the companions lose all elite seating privileges. In this case the AA agent took it upon themselves to move the companions back to 'normal' economy seats.