What the Penates guarded that the Lares did not was supply rather than place. A Roman household's Lares stayed with the house itself, protecting its threshold and its ground even as one family left and another moved in; its Penates left with the family, carried out the door when a household relocated and ceremonially installed in the new one; ancient writers describe this formal welcoming as though the gods themselves were changing address alongside their owners.
That distinction explains why the Penates, and not the Lares, could plausibly travel from Troy to Italy in the foundation legend Vergil tells. A guardian of place could not have made that journey and still meant anything; a guardian of the family's store and its continuity could, because the claim being made was that the Roman people's provision and future, not any one plot of land, had survived the fall of Troy intact. The public Penates of the Roman state, kept at Lavinium and later in Rome, carried the same logic outward from household to nation: what Rome guaranteed by tending them was its own continuity as a people, not the safety of any particular building.
The two cults were never in tension. A household owed the Lares its threshold and owed the Penates its larder, and both received offerings at the same shrine, because a Roman family understood its security as needing both a place to stand and a store to live on.