You've got to bat everybody in a position that suits their strengths and, where possible, they feel comfortable batting.
I don't think you'd see Australia wanting Smith at 3 due to his vulnerabilities against the newer ball, I hope England don't do that with Root as he's so prolific where he is. If 3 is the position, then find a top order player to do that job, don't play around with a settled, prolific middle order that has basically won the last 2 series for England.
I do however think you could get away with having Woakes & Stokes in the same side and dropping Finn which strengthens the batting further (Without really weakening the bowling in anyway) allowing for an inexperienced 3 to be given time to bed in.