A direct application of applied load/moment are the reason why we experience anything that happens within the structure (like deformations, strains, stresses etc). If not direct load/moment are applied, then nothing will happen and the body will just remain as it is. So anything that happens (for instance, warping in a rectangular shaft due to torsion, which results in tension and compression stresses as well) are a result of a direct application of load/moment. So nothing can be indirect.
Maybe the author tried to use simple words to not to confuse the audience. When you apply a transverse/lateral load to a cross section, it infers that it is a shear load since it is parallel to the cross section (and by definition, loads parallel to the cross sections result in shear stresses). I guess this is what he meant by direct load. According to this analogy, the tension and compression stresses due to warping, and even bending stresses due to transverse/lateral loads are all due to indirect loads, i.e. arising due to torsion and due to transverse/lateral loads respectively. Since it was initially taught that only an axial force could result in axial stresses (like tension and compression).
Moreover, you might also exprience shear stresses when you fix a beam on one side and apply axial force on the other. This can be a case of indirect shear stress. Think it like this, the extreme end is fixed meaning that this face cannot deform, while just its adjacent cross section is expanding/squeezing due to poisson's ratio effect in an axial loading condition. This relative deformation means that shear stress must exist.