Yep...(Agreeing with Paul)

The datum line or "waterline" is just an arbitrary reference. I think in commercial aircraft, this would most often be the "deck angle", (angle of the floor/seats) so the designers can come up with a zero or near-zero deck angle for cruise. The wing, engine, and tail parts might all have different angles, to make the thing work.

My approach to designing models, using a typical planform with a forward wing and standard or "T" tail is:

I try and calculate the lowest drag position (typically my "zero" reference) of the fuselage, and then, using known airfoil data, try and figure the wing's angle of attack at cruise speed, so that in cruise configuration, the fuselage is in it's lowest drag position. Then I mount the wing on the fuselage at that cruise-optimized position. (usually a degree or so positive for symmetrical airfoils, and usually zero or slightly negative incidence for cambered airfoils.)

I believe that stabilizer incidence is arrived at by what the "zero trim" angle for cruise would be. (to reduce drag on the stabilizer) CG variations, different airfoils, and varying airspeeds will change the amount of download on the tail too, of course, but the general idea is the same.