If ordinary and extraordinary rays emerge out of calcite crystal at different points(double refraction) then why do we consider perpendicular electromagnetic wave components shifted by a phase in case of wave plates emerge at the same point?
This is because of how wave plate is made and used. The crystal is cut so that the optic axis is parallel to the long faces. Incident rays are normal to the plate and the optic axis so there is no refraction, only retardation. Wave plates are typically very thin (about 0.1mm) so even if the angle of incidence is not zero the deviation is very small compared with the diameter of the beam.