We introduce UnIPH, an equivariant graph neural network designed to jointly predict both interatomic potentials and tight-binding (TB) Hamiltonians for an atomic structure. UnIPH is trained using density functional theory (DFT) calculations followed by Wannier projection to predict energies and forces as node-level targets and Wannier-projected TB Hamiltonians as edge-level targets. This enables physically consistent modeling of coupled mechanical-electronic responses with near-DFT-level accuracy. After separately training two UnIPH models on DFT data for bilayer graphene and monolayer MoS2, respectively, we find that these models capture key deformation-electronic effects: in twisted bilayer graphene, the trained UnIPH reveals how interlayer spacing, in-plane strain, and out-of-plane corrugation drive isolated flat-band formation, and further shows that modulating substrate interaction strength can generate flat bands even away from the magic angle (approximately 1.1 degrees). For monolayer MoS2, UnIPH accurately reproduces phonon dispersions and strain-dependent band-gap evolution, and further predicts how a non-uniform substrate creates localized strain pockets that spatially modulate the conduction- and valence-band edges.