It really doesn't matter whether the servo itself is mounted square to the wing chord or the aileron hinge line. What will matter is where you attach the aileron control horn. If you attach the horn such that the connector between the servo and the hinge line is not perpendicular, you can introduce mechanical aileron differential, which can affect performance. I normally set them up so the control rod is perpendicular to the hinge line. The next effect is where the servo neutral position is. You can normally rotate the servo arm on the servo to put it in position that the neutral position is perpendicular to the hinge line. Again, you can adjust this alignment to provide any aileron differential you may desire.

I normally mount my servos such that they are aligned with the wing chord simply because its easier to cut at fit the servo mounting at 90 degrees.

Bottom line - do what works for you.

Brad