We study the spectral properties of ergodic Schrödinger operators that are associated to a certain family of non-primitive substitutions on a binary alphabet. The corresponding subshifts provide examples of dynamical systems that go beyond minimality, unique ergodicity and linear complexity. In some parameter region, we are naturally in the setting of an infinite ergodic measure. The almost sure spectrum is singular and contains an interval. Some criteria for the exclusion of eigenvalues are fully characterized, including the existence of strongly palindromic sequences. Many of our structural insights rely on return word decompositions in the context of non-uniformly recurrent sequences. We introduce an associated induced system that is topologically conjugate to an odometer.