An AS companion fare makes absolutely no difference on the upgrade status (or mileage earned) for the passengers. The only difference is that the companion's ticket cannot be separated into a separate PNR (which may be necessary to be upgraded in your situation, if you're being upgraded on the basis of your AA status and she's being upgraded on the basis of her AS status – I do not know). The primary traveler can travel without the companion, but then the $99 fare paid for the companion is forfeit. So I'm 98% sure that the fact that you are traveling on a companion ticket makes no difference; the situation would be the same if you had two normal fare tickets on the same PNR (except that in that situation you might split the record to each get upgraded on your own merits).

I don't know what the upgrade situation is for an AS MVP and an AA PPro on one reservation on AS, but I think that, not the companion fare, is the relevant question.