The issue isn't that he moves out of position, it is how he does it and more importantly his inability to move back in to position. A natural AM already knows the pass is coming when he starts moving out to the pocket of space. When they make the move wide, the play will nearly always be there with few exceptions.
If they don't receive the ball because the team chooses another route, they run faster to get back in centrally than they did to move out to the pocket.
This means they are nearly always involved in the game, whether the team plays on the left, right or central.
Rooney usually makes runs more like a striker would, much less smooth and calculated and more opportunistic. If he gets the ball it is usually a clear-cut chance, but Rooney doesn't really take in to account how hard and likely the pass will be. The natural AM's considers how high percentage the pass will be for his team mate to decide if he should initiate it or not.
It is different roles, Mata/Kagawa can't play Rooney's role and he can't play theirs. It is just unfortunate for Rooney that our team lacks cohesion, fluidity and have a weak central midfield - the exact reasons why you play a playmaker instead of a 2nd striker.
In another team Rooney may have been exactly what was needed and Mata would get the wrong side of the stick.