Near Edge X-ray Absorption, Valence and Core-level Photoemission and Density Functional Theory calculations are used to study molecular levels of tetracyano-2,3,5,6-tetrafluoroquinodimethane (F$_4$TCNQ) deposited on Ag(111) and BiAg$_2$/Ag(111). The high electron affinity of F$_4$TCNQ triggers a large static charge transfer from the substrate, and, more interestingly, hybridization with the substrate leads to a radical change of symmetry, shape and energy of frontier molecular orbitals. The Lowest Unoccupied Molecular Orbital (LUMO) shifts below the Fermi energy, becoming the new Highest Occupied Molecular Orbital ($n$-HOMO), whereas the $n$-LUMO is defined by a hybrid band with mixed $π^*$ and $σ^*$ symmetries, localized at quinone rings and cyano groups, respectively. The presence of Bi influences the way the molecule contacts the substrate with the cyano group. The molecule/surface distance is closer and the bond more extended over substrate atoms in F$_4$TCNQ/Ag(111), whereas in F$_4$TCNQ/BiAg$_2$/Ag(111) the distance is larger and the contact more localized on top of Bi. This does not significantly alter molecular levels, but it causes the respective absence or presence of optical excitations in F$_4$TCNQ core-level spectra.