Polarization-based optical communications are attracting more attention recently, where the crucial points are polarization features and their measurements. Based on the Müller matrix method, we obtain measurable expressions for the polarization-dependent gain (PDG) and the loss of polarization orthogonality (LPO), while give the boundary of the LPO for any PDG devices. We experimentally demonstrate that non-linear LPO can be created in a semiconductor optical amplifier and find that the LPO will slightly skim over the boundary near the threshold of the injected current. Furthermore, an empirical formula is achieved to gauge the LPO-induced power penalty, which is proven to be valid in differential polarization shift-keying transmission by executing a bit error rate measurement. Our conclusions are applicable to non-orthogonal polarization cases and valuable to polarization-related communications, even orbital angular momentum multiplexing.