Kwant adds sites to the lead until it reaches the system. This doesn't mean that it duplicates the unit cell.
In fact, the band can be obtained without attaching the lead and the Hamiltonian of the unit cell can be directly obtained by:
lead.cell_hamiltonian(params=params) #(the lead needs to be finalized here)
So you can verify that the unit cell is not duplicated and it is solely defined using the base you defined for the lattice.
I hope this helps,