Universal relations among macroscopic properties of neutron stars provide a powerful framework to probe their internal structures while minimizing uncertainties associated with the equation of state (EoS). Although such relations have been extensively studied for uniformly rotating stars, their extension to differentially rotating and strongly magnetized configurations is relatively less explored. We systematically investigate equilibrium configurations for a wide range of EoSs, rotation profiles, and magnetic field strengths with XNS numerical simulation code. For sequences with fixed angular momentum, we analyze the dependence of normalized moment of inertia on compactness. We establish a generalized quasi-universal relation between the moment of inertia and compactness that remains remarkably insensitive to the underlying EoS across uniformly rotating, differentially rotating, and strongly magnetized toroidal configurations. For sequences with fixed angular momentum, the normalized moment of inertia exhibits a quasi-universal dependence on compactness, with deviations primarily due to magnetic field strength and degree of differential rotation. We derive analytic expressions for these dependencies, enabling a unified phenomenological model applicable over a wide range of stellar configurations. As astrophysical applications, we quantify the systematic bias in magnetar luminosity estimates and the rotational kinetic energy of post-merger remnant of GW170817. These results extend quasi-universal relations beyond the standard assumptions of uniform rotation and weak magnetization, providing a robust framework for interpreting observations of highly magnetized and differentially rotating neutron stars, and enabling more reliable constraints on their astrophysical properties.