OK, from the other side of the sideline:
Actually, in many cases, it DOES help to be a few steps out onto the field to call a play. Not because it puts you closer to your QB, but because it separates you from all of the other hubbub going on on the sidelines. You stand out more, the QB can see you easier, and you don't have a player or other coach in your ear while trying to signal in a play.
But I'm talking about ONE coach being a step or two on the field. If that's all it is, AND the coach is out of the restricted area before the ball is snapped, leave it alone and don't go looking for trouble. There will be plenty of it other places. Worrying about this gets you a reputation of being overly officious and antagonistic.
Of course, if the coach is abusing it, a friendly request (without an incorrectly used sideline warning flag) will usually put an end to the abuse. Believe it or not, most coaches don't go looking to be confrontational, and if approached in a friendly manner rather than ordered, they will try to cooperate.
If coaches in your area have NOTHING to do with your future through ratings or contract awards or complaints, then by all means, be a j#rk about it. But in most places, they DO have input, either formally or informally, and establishing a good WORKING relationship with your sideline is beneficial to you and the game.