The reconfigurability of radio environments with programmable metasurfaces is considered a key feature of next-generation wireless networks. Identifying suitable metasurface configurations for desired wireless functionalities requires a precise setting-specific understanding of the intricate impact of the metasurface configuration on the wireless channels. Yet, to date, the relevant short and long-range correlations between the meta-atoms due to proximity and reverberation are largely ignored rather than precisely captured. Here, we experimentally demonstrate that a compact model derived from first physical principles can precisely predict how wireless channels in complex scattering environments depend on the programmable-metasurface configuration. The model is calibrated using a very small random subset of all possible metasurface configurations and without knowing the setup’s geometry. Our approach achieves two orders of magnitude higher precision than a deep learning-based digital-twin benchmark while involving hundred times fewer parameters. Strikingly, when only phaseless calibration data is available, our model can nonetheless retrieve the precise phase relations of the scattering matrix as well as their dependencies on the metasurface configuration. Thereby, we achieve coherent wave control (focusing or enhancing absorption) and phase-shift-keying backscatter communications without ever having measured phase information. Finally, our model is also capable of retrieving the essential properties of scattering coefficients for which no calibration data was ever provided. These unique generalization capabilities of our pure-physics model significantly alleviate the measurement complexity. Our approach is also directly relevant to dynamic metasurface antennas, microwave-based signal processors as well as emerging in situ reconfigurable nanophotonic, optical and room-acoustical systems.