Why should it do that? You shouldn't be able to manipulate the teams that get assigned, as that's not the point of autodeploy. If you want to control what teams are assigned, just assign them yourself.
Also, different people use the favorite tag for different things. I use it for units I'm farming to make it easier to find the nodes. Other people use it for characters they're working on gearing. There is no reason whatsoever that those characters should be placed first.