Single-photon transitions are one of the key technologies for designing and operating very-long-baseline atom interferometers tailored for terrestrial gravitational-wave and dark-matter detection. Since such setups aim at the detection of relativistic and beyond-Standard-Model physics, the analysis of interferometric phases as well as of atomic diffraction must be performed to this precision and including these effects. In contrast, most treatments focused on idealized diffraction so far. Here, we study single-photon transitions, both magnetically induced and direct ones, in gravity and Standard-Model extensions modeling dark matter as well as Einstein-equivalence-principle violations. We take into account relativistic effects like the coupling of internal to center-of-mass degrees of freedom, induced by the mass defect, as well as the gravitational redshift of the diffracting light pulse. To this end, we also include chirping of the light pulse required by terrestrial setups, as well as its associated modified momentum transfer for single-photon transitions