Incidence is the angle between some arbitrary reference line, like the centerline of the fuselage, and the chord line of a flying surface like a wing or tail. The purpose of incidence is to make it easier to establish the angular relationship between the wing and tail in order to rig the plane for initial flight. After that the arbitrary reference line is never used directly again because its location can only be found in reference to chords and thrust lines. It serves the same intermediary purpose for establishing the angular relationship betweeen the thrust line and the wing chord line. The aerodynamic significance of the centerline of the fuselage (or any other arbitrary reference line) is not nearly as great as the decalage (angle between the wing and tail) or the thrust line to the wing and tail chords.

There is a range of acceptable CG's on any plane. The best location of the CG within that range depends on the purpose of the plane, the skill level of the pilot and the flying style of the pilot. Trimming the plane for the best CG also requires trimming the decalage. This usually is done with a click ot two of elevator trim which changes the camber and incidence of the horizontal tail. Most people would rather live with the minor offset in the elevator rather than remount the wing or tail so that the elevator would be perfectly aligned to the stabilizer geometrically.

Make no mistake. Trimming a plane involves adjusting the decalage one way or another. Exactly the same thing could be said of thrust line adjustments.
Incidence and thrust alignment to an arbitrary reference line during building and initial rigging makes the plane ready for safe flight testing to prepare it to change those angles a bit as the plane is tuned to its purpose and pilot.