A thrustline offset is used because a permanent trim position of a flight surface changes effect as airspeed changes. A thrustline offset is used to compensate for how the engine pulls the airplane. With a lot of power, you get a lot of compensation, and with a little power, little compensation.

Even full-size aircraft have thrustline offsets. Witness the Aircoupe, with a lot of right and downthrust.

Downthrust is used to minimize pitch changes with throttle changes, and sidethrust (usually to the right) is used to minimize how much the engine pulls the airplane left or right as power changes.

Ideally, you want the aircraft to have the flight surfaces trimmed for neutral when in level flight at your desired "cruise" airspeed and throttle setting. For an aerobatic model with a fully-symmetrical airfoil, you'll of course have a bit of 'up' elevator in upright level flight, and need a bit of 'down' elevator in level inverted flight. Rudder and ailerons should be in their neutral positions, in trail with the main surface. Otherwise, the model will have a tendency to roll or yaw in varying amounts, depending upon the airspeed.

Some aerobatic models, because of their force layout actually have the engine positioned with some 'up' thrust in order for them to have the desired aerobatic characteristics.

It all comes down to handling. Adjusting of the thrustline is one of the many different things you may have to do to get your model to handle just they way you want it...just like you have to adjust wing and stabilizer angles with respect to the fuselage and each other, altering dihedral angles, and so on. Top-level fliers and designers work with their models, tweaking them until they perform just how they want them to perform.