Maybe I am misunderstanding the issue here, but FWIW my recent experience:
Flight 1, YWG-YYC booked with Ms SWMBO Stanbury's stash of points. I am the only passenger on the PNR. Her AE number is on my file, and I cannot edit it. However, at online check in I see her AE number, I click on it, I am allowed to edit it, I do so, and I get my Elite50K MM privileges (which amount to zone 2 boarding -- useful as it was a Q400).
Flight 2, YYC-YWG, again booked with Ms SWMBO Stanbury's points, travelling together, on same PNR. Again, I can do nothing until online check-in, at which time there is a blank in my AE number field which I can edit to contain my AE number. Again I get zone 2. And as an aside, we had no problem each checking a bag for free.
Sorry if this is irrelevant to the discussion, but it seems to run counter to what others are experiencing and reflects what I have/have not been able to do each time I use her points ...
... which I do as mine have been essentially -- and wisely I think -- depleted with a number (8 or so) of recent TATL BIZ flights -- but that's another topic.