Mueller matrix ellipsometry has been used to precisely characterize quartz waveplates for demanding applications in the semiconductor industry and high precision polarimetry. We have found this experimental technique to be beneficial to use because it enables us to obtain absolute and precise measurement of retardation in a wide spectral range, waveplate orientation, and compound waveplate adjustment. In this paper, the necessity of including the optical activity in the Mueller matrix model and data treatment is demonstrated. Particularly, the optical activity of the quartz influences the adjustment of misalignment between the perpendicularly oriented waveplates of the compound biplate. We demonstrate that omitting the optical activity from the model leads to inaccurate values of the misalignment. In addition, the depolarization effects caused by a finite monochromator bandwidth is included in the model. Incorporation of the optical activity to the Mueller matrix model has required a development of rigorous theory based on appropriate constitutive equations. The generalized Yeh's matrix algebra to bianisotropic media has been used for the calculation of the eigenmodes propagation in chiral materials with reduced symmetry. Based on the applied method, the authors have proposed approximated analytical form of the Mueller matrix representing optically active waveplate and biplate and provided discussion on the analytical and numerical limits of the method.