<p>Active molecular motors coordinate their action to reorganize on fluid membranes to drive faster or more efficient cellular transport. The resulting membrane hydrodynamics have been shown to enhance in-plane transport and guide self-assembly. In this work, we examine the qualitative differences that arise in the collective motion of active, force-free inclusions as a result of ‘confining’ the extent of the 3D fluid phase adjacent to the membrane. A thin film underlying the membrane screens hydrodynamic interactions and modifies the effective Saffman-Delbrück length. We characterize resulting features in cluster formation and lipid-field reorganization using large-scale simulations. We also analytically investigate the stability of typical aggregate structures seen in simulations, demonstrating the role of hydrodynamic interactions modulated by the extent of bulk phase in driving aggregation and reorganization in the plane of the membrane. Put together, we reveal new mechanisms of driving lipid transport and coordinated motion by modulating collective activity within membranes.</p>