The Martian moon Phobos is becoming an appealing destination for future scientific missions. The orbital dynamics around this planetary satellite is particularly complex due to the unique combination of both small mass-ratio and length-scale of the Mars-Phobos couple: the resulting sphere of influence of the moon is very close to its surface, therefore both the classical two-body problem and circular restricted three-body problem (CR3BP) do not provide an accurate approximation to describe the spacecraft's dynamics in the vicinity of Phobos. The aim of this paper is to extend the model of the CR3BP to consider the orbital eccentricity and the highly-inhomogeneous gravity field of Phobos, by incorporating the gravity harmonics series expansion into an elliptic R3BP, named ER3BP-GH. Following this, the dynamical substitutes of the Libration Point Orbits (LPOs) are computed in this more realistic model of the relative dynamics around Phobos, combining methodologies from dynamical systems theory and numerical continuation techniques. Results obtained show that the structure of the periodic and quasi-periodic LPOs differs substantially from the classical case without harmonics. Several potential applications of these natural orbits are presented to enable unique low-cost operations in the proximity of Phobos, such as close-range observation, communication, and passive radiation shielding for human spaceflight. Furthermore, their invariant manifolds are demonstrated to provide high-performance natural landing and take-off pathways to and from Phobos' surface, and transfers from and to Martian orbits. These orbits could be exploited in upcoming and future space missions targeting the exploration of this Martian moon.