As Tom C points out, it is relatively easy to change things on a stick type model. On models with a long tail it is relatively easy to manage. I have a Trainer 60 that is set up as a sport model and it is not very noticeable. On the other hand I have a Staggerwing Beech that is proving to be a handful and needs the right thrust along with a gyro. With a stick model places where I notice the difference are on take off and on pulling vertical. At those times there is a tendency to yaw left. I've never been a pattern flier but I recall reading articles on how to add right thrust a degree at a time to tune a pattern plane to maintain a vertical line under power. With down thrust you can think of the distance between the centerline of the wing and the thrust line of the engine as the arm of a lever. If they are close together then the lever is short and the drag of the wing and the thrust of the wing won't cause much pitching force. If the two lines are far apart (think Piper Cub) then the engine wants to pull the airplane around the drag of the wing. You can change the thrust line to control for this. Where I have experienced it most often is in high wing aircraft that want to pitch up under power. On a shoulder wing it shouldn't be as big of a thing. There is a ton of info out there on model aircraft design.
The short answer is that I would suggest going with the factory settings since you can take the offset out with shims if you don't like it.