Imagine 2 theoretical planes, A and B, shown in the image below. The center of mass is yellow, and the center of lift is blue. Would plane A and plane B work as well as an airplane with the center of lift in line with the center of mass or no?
In my opinion the vertical position of the center of gravity (CG) is negligible. First of all the variation will be very small. Between an airplane with lead on the bottom of the cargo and an airplane with all passengers on the upper deck the CG will not move that much. And statistically the CG will probably be somewhat around the centerline of the fuselage. Then, yes drag forces and engine thrust could create a tiny pitching moment but the leverage will only be a few inches at max thus the moment being very small compared to the gravity VS lift pitching moment resulting from the horizontal distance between CG and CP.
In the end question is somewhat similar to : "what's better low or high wing planes?". On one side CG is above or near the wings and on the other hand way below the wing. Both works fine and requires only small design variations for aerodynamics stability.
What is missing from the diagram is the vectoral representation of the Center of Lift. Unlike the center of Mass, which is just a point within the aircraft. the Center of Lift or the Aerodynamic Center, is meaningless unless you also show the direction that the vector sum of all aerodynamic forces is acting in. You cannot know whether the Aerodynamic force is "in line" with the Center of Mass unless you know what direction the Aerodynamic forces are acting in. For example, if the the vector sum of all aerodynamic forces is acting through the blue dot but pointing straight back, then it's extension will pass above or below the Yellow (CG) dot based on where the blue dot is vertically located. In both locations for the blue dot, if the aerodynamic force vector is oriented so that it passes THROUGH the yellow dot, there will be NO pitching moment, no matter where it is located vertically.
Since in most aircraft, the Aerodynamic center is behind the CG, and in normal straight and level flight, the vector must of course be pointed upwards and slightly aft (due to the drag component), the vertical position of the Center of Pressure will have only a minor impact on the static margin. The term "Static Margin" is often used to describe this phenomenon. It is a measure of the distance between the extension of the Aerodynamic force vector and the position of the center of Mass. The lower the static margin, (the closer the vector is to the CG), the less stable the aircraft is and the more the trim forces are required to keep it in balance.