She seems to have a preference of red mechs, according to M7. When Gamlin crashed her VF-1J, she had her VF-17 painted red before she piloted it.
It would seem to me that the couple kinda went rogue after Max disappeared. I would doubt that he got a hold of the Macross and asked to fly for the Meltrans. As for the blue uniform and blue Q-Rau? Who knows how the hell they got a hold of that. Maybe it was from a dead Ace (like Millia) waiting to be cloned. I can't imagine Max asking for a custom color and the uniform did make him look a little feminine, with the wide hips look and all.
Maybe morally he wasn't a traitor, but what would you call someone that donned the enemy's uniform and flew the enemy's battle craft?
In the TV series, Millia was lucky they saw her wedding and sent Exedol. If not who's side would she be in? I know she wouldn't destroy the Zentraedi battle Pods, but disabling them was still an act of treason.
You never know... things could have changed by then. A pink valk wouldn't be very fun. <_<