The recent observation of superconductivity in proximity to an insulating phase in twisted bilayer graphene (TBG) at small "magic" twist angles has been linked to the existence of nearly flat bands, which make TBG a fresh playground to investigate the interplay between correlations and superconductivity. The low-energy narrow bands were shown to be well described by an effective tight-binding model on the honeycomb lattice (the dual of the triangular Moiré superlattice) with a local orbital degree of freedom. In this paper, we perform a strong-coupling analysis of the proposed px,py two-orbital extended Hubbard model on the honeycomb lattice. By decomposing the interacting terms in the particle-particle and particle-hole channels, we classify the different possible superconducting, magnetic, and charge instabilities of the system. In the pairing case, we pay particular attention to the two-component (d-wave) pairing channels, which admit vestigial phases with nematic or chiral orders, and study their phenomenology. Furthermore, we explore the strong-coupling regime by obtaining a simplified spin-orbital exchange model which may describe a putative Mott-type insulating state at quarter-filling. Our mean-field solution reveals a rich intertwinement between ferromagnetic and antiferromagnetic orders with different types of nematic and magnetic orbital orders. Overall, our work provides a solid framework for further investigations of the phase diagram of the two-orbital extended Hubbard model in both strong- and weak-coupling regimes.