Thank you Adel and Christoph! 
sym.add_site_family(lat, other_vectors=[v]) with v orthogonal to the 
translation symmetry vector places the lead in the way I expected. 
Still, there are one supercell's extra sites added in blue connecting the 
original central region and the lead 
(https://www.dropbox.com/s/3c1uioclcbsez4g/lattice2.pdf?dl=0). If I put 
disorder in the central region, I presume these added sites although in blue 
color will be the same as the lead Hamiltonian and thus do not have disorder? 
If so, I guess it might only very slightly affect the physics once the central 
region is not too small. And these extra sites are currently unavoidable?

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