Andy Lennon says in RC Model Aircraft Design that a high thrust line is stabilising and that a low thust line is destabilising. However I think this really depends on the aircraft in question. My personal preference is for engines whose thrustline is directly through the wing and tail - they seem to be the most controllable, neutral and flyable.

I doubt whether the change you are talking about will have a significant impact on flying the model.

As beepee says to ensure that the thrust line goes through the centre of drag with a lower thrust line you could add some downwash.