No, this is not possible: The design concept for punching shear design provides for a static depth d that is constant along the critical perimeter. The orthotropy specification (for example, "effective thickness") contradicts this design concept. Therefore, it is not possible to select the nodes of punching shear in the surfaces with orthotropic stiffness.
If you still want to design a plate with the "Orthotropic" stiffness type, you would have to perform the punching shear design in RF‑PUNCH Pro using a copy of the file with the surfaces, where you change the stiffness type to "Standard". In Window 1.5 of RF‑PUNCH Pro, apply a user-defined punching load, which would result from the structure with the orthotropic surfaces.