A variational model for the interaction between homogenization and phase separation is considered. The focus is on the regime where the latter happens at a smaller scale than the former, and when the wells of the double well potential are allowed to move and to have discontinuities. The zeroth and first order Gamma -limits are identified. The topology considered for the latter is that of two-scale, since it encodes more information on the asymptotic local microstructure. In particular, when the wells are non-constant, the first order Gamma -limit describes the contribution of microscopic phase separation, even in situations where there is no macroscopic phase separation. As a corollary, the minimum of the mass constrained minimization problem is characterized, and it is shown to depend on whether or not the wells are discontinuous. In the process of proving these results, the theory of inhomogeneous Modica Mortola functionals is strengthened.
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