Transfer alignment is an effective method to estimate the attitude difference between two inertial platforms. Traditional transfer alignment methods are either meant for small misalignments or use nonlinear filtering. Linear methods for large misalignments use quaternion attitude representation, but their performance degrades when the misalignment is not constant or slowly varying. This work proposes to apply rapid transfer alignment to the inertial stabilization of a Satcom On The Move antenna. In this application case, the two inertial platforms are connected by a kinematic chain, meaning the attitude difference between the inertial platforms is both large and time-varying. This work proposes a method to estimate this attitude difference. A linear Kalman filter is used for the estimation of the unknown angles. To that effect, a new propagation model is developed to take into account the misalignment variations using master and slave rotation rates. Simulation results show the performance of the proposed solution in a Satcom antenna inertial stabilization case.