Transverse stratification is a common intrinsic feature of astrophysical jets. There is growing evidence that jets in radio galaxies consist of a fast low-density outflow at the jet axis, surrounded by a slower, denser, extended jet. The inner and outer jet components then have a different origin and launching mechanism, making their effective inertia, magnetization, associated energy flux, and angular momentum content different as well. Their interface will develop differential rotation, where disruptions may occur. Here we investigate the stability of rotating, two-component relativistic outflows typical for jets in radio galaxies. For this purpose, we parametrically explore the long-term evolution of a transverse cross section of radially stratified jets numerically, extending our previous study where a single, purely hydrodynamic evolution was considered. We include cases with poloidally magnetized jet components, covering hydro and magnetohydrodynamic (MHD) models. With grid-adaptive relativistic MHD simulations, augmented with approximate linear stability analysis, we revisit the interaction between the two jet components. We study the influence of dynamically important poloidal magnetic fields, with varying contributions of the inner component jet to the total kinetic energy flux of the jet, on their non-linear azimuthal stability. We demonstrate that two-component jets with high kinetic energy flux and inner jet effective inertia which is higher than the outer jet effective inertia are subject to the development of a relativistically enhanced, rotation-induced Rayleigh-Taylor-type instability. This instability plays a major role in decelerating the inner jet and the overall jet decollimation. This novel deceleration scenario can partly explain the radio source dichotomy, relating it directly to the efficiency of the central engine in launching the inner jet component. The FRII/FRI transition could then occur when the relative kinetic energy flux of the inner to the outer jet grows beyond a certain threshold.