We present a study of the expectations for very-high-energy (VHE) to ultra-high-energy (UHE) gamma-ray and neutrino emission from interacting cosmic rays in our Galaxy as well as a comparison to the latest results for the Galactic UHE diffuse emission. We demonstrate the importance of properly accounting for both the mixed cosmic-ray composition and the gamma-ray absorption. We adopt the wounded-nucleon model of nucleus interactions and provide parameterisations of the resulting gamma-ray and neutrino production. Nucleon shielding due to clustering inside nuclei is shown to have a measurable effect on the production of gamma rays and is particularly evident close to breaks and cutoffs in mixed-composition particle spectra. The change in composition around the 'knee' in the cosmic ray spectrum has a noticeable impact on the diffuse neutrino and gamma-ray emission spectra. We show that current and near-future detectors can probe these differences in the key energy range from 10 TeV to 1 PeV, testing the paradigm of the universality of the cosmic ray spectrum and composition throughout the Galaxy.