^ I think they've said in the past that player complaints about walking around as a mage without any attention were noted. A lot of people particularly disliked the lack of reactivity to doing blood magic openly in the street, and it's something they promised to look at for DA:I.
Supposedly there was a conversation planned for the early part of DA2 where you'd come to an agreement with the guards or Merideth to be left alone (I forget exactly who it was now), but it didn't make it into the game due to time or resource constraints.
So I don't think it was a deliberate move to ignore the 'apostate' mages in the party, just something that reflected the lack of time they had to do many things in DA2.
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EDIT: But of course, in DAI any mages that accompany the player get whatever privileges the world is giving the Inquisition generally, so I doubt anybody except the qunari would kick up a fuss about mages in the party.
And that concept art does show mages being attacked by the Templars. We shouldn't assume that just because Hawke's mage party members got immunity by virtue of being special plot snowflakes, that *every* mage in the world will be protected. The player's companions are all freakishly unusual people, and the plot will bend to accommodate the player in ways that don't apply to every other person in the DA universe.