Definition of aircraft longitudinal axis?
Aircraft designers use many different axis frames, depending on what is the most convenient under the circumstances.
In the context of the question, I need to mention only two of them, or rather even - two classes of them: body axes and wind axes.
The body frame is tied, well, to the body. It is rigidly fixed to the body and moves with it. By convention, the X axis points &quot;forward&quot;, to the nose.
The wind frame is aligned with the streamflow &quot;at the infinity&quot;, and its X axis points against the free stream. If you rotate the wind frame by the wind angles - angle of sideslip and angle of attack - you get to the body frame.
The term &quot;longitudinal axis&quot; refers specifically to the body X axis.
But where is the origin? It depends!
For most calculations, especially in flight mechanics, it is best to put the origin at the centre of mass. Furthermore, the direction of the longitudinal axis, over which the designer has some liberty (that arbitrary &quot;forward&quot;), should be such that it formed (one of) the principal axis of rotation.
This is not always easy, nor necessarily convenient. Centre of mass moves, the aircraft may not be symmetric, and the airframe designer will not like the reference axes moving about.
To avoid ambiguity, it is often necessary to state in which system the calculation is done, and how exactly it is defined. Oftentimes, engineers in a certain sub-field (e.g. flight mechanics) assume a certain frame and understand each other well, but this assumed knowledge is not carried to other fields, leading to errors and misunderstandings.
The situation is exacerbated by the fact that in many practical cases, the difference between the frames seems to be small, and the result may be &quot;approximately correct&quot; in most of them.1
So, as a designer, you decide how you define the longitudinal axis. If the aircraft is relatively symmetric, draw it as the axis of symmetry.
Your choice will affect how you read angle of attack (AoA). There is nothing strange about that: AoA of the aircraft is also &quot;conventional&quot;: it is with respect to an essentially arbitrary axis. It will likely be different to the AoA of the wing, which is of the most concern for the aerodynamicist. (One of the conventions in pure aerodynamics is to choose the X direction such that it resulted in zero lift at zero AoA).
Whether the airflow will align with the axis at cruise depends on your choice. You will need to choose the angle of incidence of the wing to minimise drag, but the AoA may not be zero if you chose the axis direction with other considerations in mind.
Note that the choice of origin will not affect the wind angles. Essentially, you can leave the choice of origin until you need to decide on the other two axes.

1 A common example: Lift is defined in the wind axes. It is normally linearly dependent (~proportional) on AoA, but this only holds perpendicular to wind, and not with respect to &quot;up&quot; of the aircraft. But the difference is small for small angles.