Dual-drive H-type gantry stages, powered by direct-drive linear motors, are commonly used in precision industrial applications that require high positioning accuracy over a large workspace. The cross-arm rigidly couples the two parallel axes, making strict synchronization control essential for maintaining positioning accuracy. Conventional master-master control treats the coupling effects as disturbances without accounting for the synchronization of the two motors. As a result, its performance deteriorates significantly under non-uniform load distribution, payload rotation, and directly applied torque disturbances, all of which necessitate reliable synchronization control. This study proposes a synchronization control scheme that integrates a sliding-mode controller with an uncertainty and disturbance estimator (SMC-UDE) and a feedforward torque compensator for the inertial torque induced by payload rotation. The proposed controller was implemented on a Hardware-in-the-Loop (HIL) simulator constructed with two parallel voice coil motors, and its performance was experimentally validated on the testbed. The HIL experimental results demonstrate that the SMC-UDE controller with feedforward torque-disturbance compensation achieves a quicker settling time compared to the conventional master-master control strategy. Additionally, it effectively suppresses disturbances generated by a rotary motor attached to a payload, thereby maintaining synchronization accuracy under disturbed conditions.