OK, so I think I finally have some clarity now that we are <24 hours from departure. The latest AS agent I spoke with gave the best response and the response I believe to be the most plausible. Essentially it boils down to this: oneworld Emeralds are not able to complimentary upgrade a companion at this time. Full stop, it doesn't mater what type of fare you are on. Upgrades using miles are possible (as I did on my outbound flight), but no complimentary upgrades for companions of Emeralds and that means if you are on a linked reservation no upgrades for the Emerald either.

So this means that since I am on a linked reservation (that can't be unlinked due to Companion Fare) even if multiple U fares became available at once I (we) would be passed over since I am not able to upgrade my companion. They said this is why my (our) name(s) did not show up in the upgrade list. This tracks with why my wife's name was not on the list either as she is just MVP and also unable to upgrade a companion, but she would be able to upgrade herself if she was on a solo ticket. So this seems to make sense and explain everything.

The agent said that ones the companion upgrades go into effect (AA says later this year) then it should place my name on the list and have a "(2)" with the reservation and be able to upgrade us both if the right amount of U fares become available. They said it would not matter if fare had a Companion Fare or whether the Emerald was booked as the primary passenger or under the Companion Fare.

Unfortunately, in this case we couldn't use miles to upgrade this flight as the U fares only became available after check-in, and they were automatically matched to 2x 1M milers and 2x 100/75K. This left 1 seat left open and 20 names on the list below that. I guess this is the way it should work, and we should be happy that their AS loyalty is being rewarded instead of someone else sneaking in and nabbing the upgrade with some miles. The agent said I would have been 5th on the list if I didn't have a companion.

Anyway, I think we finally have some clarity and closure to the situation as it stands currently. Hopefully we'll see the "later this year" clause dropped soon and the ability to upgrade companions be rolled out. Good luck to others, and I look forward to hearing a success story before my next planned trip on AS around Christmas!