Under specific synthesis conditions the crystallization of a dense silica zeolite (TON) is followed by its in situ transformation into a less dense and, in the absence of occluded species, less stable zeolite (ITW). Periodic ab initio calculations including energy corrections for van der Waals interactions as well as zero-point and thermal effects are used first to assess the relative stability of both SiO2 (calcined) phases and then to investigate host guest interactions in the as-made zeolites, as well as their relative stability. The less dense SiO2-ITW is less stable than SiO2-TON, with an energy difference that is significantly larger than expected from their difference in molar volume. This extra destabilization is ascribed to the strained double 4-ring units of silica tetrahedra (D4R). Regarding the as-made materials, the organic cation fills in more efficiently the zeolitic voids in ITW than in TON, bringing about a larger stabilization in the former owing to the extension of the long-range addition of dispersion force contributions. On the other hand, fluoride induces a polarization of the silica framework that is highly localized in TON (showing pentacoordinated [SiO4/2F](-) units) but has a large global character in ITW (where fluoride is encapsulated into D4R units). We argue that the structure-directing role toward D4R materials that has been proposed for fluoride consists fundamentally in the ability to induce a global polarization of the silica framework that allows relaxation of the strain associated with these units. In this sense, fluoride stabilizes the otherwise strained D4R-SiO2 frameworks making them reachable for crystallization. This work documents a case in which the structure directing agents "choose" a structure not kinetically but through stabilization.