In my experience - the only PNR you would have if you booked on UAL would be UAL's PNR. However it is true that Having done this several times, I find you need to use the AC flight #'s when requesting seat assignments on AC.HOWEVER it's also true that if UAL doesn;t assign the seats when you book online, it is like pulling teeth to get them from AC> My understanding is that once UAL's allotment of seats is gone, they can't even see other seats, and while AC can see the seats, they are VERY loath to give them out. So it may be non standard but it seems to be an across the board policy.