Actually I think the relevant response is to realize that as non-EXP, the companion can't be upgraded on an award ticket (first answer!). So when calling to "link" the reservations and get MCE seats, also ask for your upgrade be un-requested. An upgrade can only be a hassle in this case (where sitting together is preferable to the upgrade).

As a side note, I notice from the original post that the passenger with status was in 5A and the non-status companion was in 5B. Never do this. If you are in a situation where there's a chance that one of you gets upgraded and one doesn't, always put the higher-status passenger in the worse seat (5B, a middle, in this case) and the lower status passenger in the better seat. That way if the higher-status passenger gets upgraded, the lower-status passenger is left with the better seat. Of course if neither of you gets upgraded you can switch if it's preferable.