Yes, the lineup of the motor's output shaft regardless of if it's a piston engine or an electric motor or the shaft on a gear drive automatically is along the thrustline. They are one and the same other than one is a real piece of metal and the other is an imaginary line through the middle of that metal.

For a 3D model it's common to start with the motor zeroed in both directions so that the thrust line is parallel to the centerline of the wing's airfoil. Electric 3D models just don't need any thrust offset.

Other styles of model will often call for small amounts of down and right thrust depending on a lot of factors.