Shape optimization typically involves geometries characterized by several dozen design variables and a possibly high number of explicit/implicit constraints restricting the design space to admissible shapes. In this work, instead of working with parametrized CAD models, the idea is to interpolate between admissible instances of finite element/CFD meshes. We show that a properly chosen surrogate model can replace the numerous geometry-based design variables with a more compact set permitting a global understanding of the admissible shapes spanning the design domain, thus reducing the size of the optimization problem. To this end, we present a two-level mesh parametrization approach for the design domain geometry based on Diffuse Approximation in a properly chosen locally linearized space, and replace the geometry-based variables with the smallest set of variables needed to represent a manifold of admissible shapes for a chosen precision. We demonstrate this approach in the problem of designing the section of an A/C duct to maximize the permeability evaluated using CFD.