Incidence -is- arbitrary. A designer selects some point on the plane, or off.. In full scale, a "waterline" designated WL00 is where everything else is mearsured from.
Usually this is well below the fuselage with the landing gear extended.
The incidence (of the wing) is important relative to the incidence of the horizontal. For ease of use, it's common practice to set the horizontal at 0 degrees incidence. The arbitrary fuselage reference line (FRL) then is placed parallel to the fore and aft extended chord of the horizontal.
For optimum aerodynamic performance, generally at a chosen weight condition and airspeed, the wing is set relative to this FRL for most efficient use of the wing.
Models seldom have the speed range between takeoff, landing and cruise/highspeed flight that full-scales experience, so precise determination of the wing angle is usually determined first by what has worked, and second by flight testing, with the elevator trimmed off 0 (faired with horizontal) as the situation requires.
On this factory drawing of the T-28, the FRL goes thru the motor, parallel to the horizontal. The motor has signifioant downthrust, and the wing significant positive incidence.
But essentially, a line is placed for reference. It might be no more than the bottom of the sheet the plan is drawn on, the horizontal drawn parallel to this, and everything else fitted.
For example, on the Lockheed S3A, the WL00 was placed 200 inches below the lowest part of the airplane., if memory serves. Why? Who knows.
As long as all measurements are done properly from that point, it's a moot question.