Incidence can be measured against any arbitrary line. That line can be selected due to influences based on what the aircraft mission would be.

For an airplane optimised for cruising, the zero line would be set along the axis of the fuse that results in minimum fuse drag. Then the wing incidence would be set at the angle of attack typical for cruise so that both wing and fuse are in their best position. That's how you would do it for a sailplane.

For aerobatics, the zero line is more arbitrary, but would run somewhere in the region of the line from the engine crank to the stabilizer, or some other way of setting a central line for the fuse. In this case, it is the relationship between the wing, thrust, and tail angles that is most important, so the datum on the fuse is not a critical choice.