For what it's worth: you do not need to book on the same PNR or have the PNR's linked in order to do this. Many times, I've booked my own ticket through a corp travel agency (had to, for the corp discount) and then either bought a separate ticket for my wife or redeemed an award. There has never been a problem with having AA issue us both premium coach seats, check in at the F counter, pre-board, etc. We have even gone through an elite security checkpoint together without hassle.

I don't know if they automatically link the PNR's when I upgrade us both. But I've called many times with two separate PNR's and had us both upgraded - no problems.

My point is: if separate PNR's is what you need to do in order to get the best airfares or to get her seat as an award, you can do that without fear of getting poor airport treatment or losing benefits. You never need to make a specific call to AA just to get the PNR's linked - if they are doing it behind the scenes on seat assignments, so be it...