If there is a center of symmetry in the unit cell and the origin for the calculation can be placed at that point then the sine series goes to zero and the complex number is eliminated. The fact that F can be negative or positive is not detectable in the X-ray experiment. The only thing that we measure with a detector is the intensity or magnitude. Therefore, squaring F eliminates its sign. The result of numerous stacking faults or small domain sizes is known as particle size broadening and can be inferred from the peak widths.
Peaks become broader with as coherent scattering domains become smaller.
This is expressed by the Scherrer Equation which assumes all reflections along a line normal to the reflecting plane. Under ideal conditions all the diffraction takes place at the Bragg angles of reflection. Bragg reflection cannot occur from a single scattering center. At the same time F is small away from the Bragg angle. In other words the peaks are very intense and narrow.