I'm oversimplifying, but I see the fuselage as simply a mechanism for mounting the wing, tail, and motor relative to each other. The important thing to consider is that to fly at a specific airspeed, the wing and horizontal stabilizer need some relative incidence. We [usually] change the relative tail incidence with elevator movement. (I'm ignoring thrust, drag, airfoil, CG, mass, and lots of other things here ... they exist but assume you are just changing wing/tail incidences.)
It can be nice to design in specific relative angles so that the airplane will cruise at it's "happy" speed with little amount of elevator deflection. Otherwise you may end up with a design that needs a lot of elevator trim for level cruise at the flight speeds you want.
(Again, over simplifying but...) how you set this up also affects how the airplane looks in the air. Does it cruise tail high (looking like it's wanting always dive) or does it cruise tail low (looking like it's always floundering/plowing through the air)?
I think the main goals of building a little bit of incidence into the wing mount is to minimize the amount of elevator trim needed in normal cruise flight and also to make the airplane look right as it's flying through the air.
Factoring in thrust line incidence, the goal of changing your thrust line is to allow a wide variety of throttle settings without affecting the pitch or roll trim too much. This is why you'll often see a motor mounted with a little down and right thrust.
This is where it can be really fun as a designer to go through multiple iterations. You can observe how your first prototype flies, and then design improvements for the next version. How the airplane flies through the air is a combination of all the above factors, and the workmanship of the builder, and the pilot's stick inputs. Trimming the aircraft out is a very important aspect of the overall flight experience.