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The computation of the entanglement entropy for inhomogeneous free fermions chains based on $q$-Racah polynomials is considered. The eigenvalues of the truncated correlation matrix are obtained from the diagonalization of the associated Heun operator via the algebraic Bethe Ansatz. In the special case of chains based on dual $q$-Hahn polynomials, the eigenvectors and eigenvalues are expressed in terms of symmetric polynomials evaluated on the Bethe roots.