We study the phase separated state of an ultracold atomic Fermi gas confined in a three-dimensional quantum harmonic trap with a BCS pairing interaction. Examining various finite-temperature phase diagrams, we investigate the interplay between the filling of the quantum trap energy levels and the pairing energy. We find that a low (high) filling leads to a large (small) critical population imbalance for the superfluid/normal transition, together with a fully (partially) polarized normal part. We also show that the decrease of the density leads to a changeover of the shape of the superfluid core from an equipotential form to a deformed one. Moreover, we clarify the intrinsic mechanisms that lead to the deformation, providing a unified scenario for phase separation and deformation in a trapped Fermi gas, allowing for a possible interpretation of the apparently controversial experimental findings.