Inelastic neutron scattering (INS) spectra of} correlated $4d$-$4f$ multiferroic oxides are difficult to interpret because magnetic, crystal-field, and lattice excitations frequently overlap in energy. The hexagonal 6H perovskite Ba${}_3$HoRu${}_2$O${}_9$ provides an ideal platform to investigate this interplay owing to the coexistence of Ru${}_2$O${}_9$ molecular units and localized Ho${}^{3+}$ moments. To identify the contributions from these different excitations, we combine INS with linear spin-wave calculations, crystal-field analysis, Raman spectroscopy, and machine-learned force field (MLFF) phonon calculations. A magnetic excitation below 6.2~meV, observed only in the low-temperature magnetic phase, is reproduced by linear spin-wave theory a collective spin-wave excitation of the coupled Ru-Ho magnetic network. At higher energies, broad excitations centered near 20, 39, 70, and 90~meV are observed that persist far above the magnetic ordering temperatures. The magnetic part of the 39~meV excitation, isolated by subtracting the Bose-corrected high-temperature data, follows the Ho${}^{3+}$ magnetic form factor. Crystal-field calculations based on the Stevens formalism place a group of strong Ho${}^{3+}$ transitions in this energy range, while Raman spectroscopy and MLFF phonon calculations identify optical phonons with comparable energies. Together, these complementary results show that the broad INS feature near 39~meV arises from overlapping Ho${}^{3+}$ crystal-field excitations and lattice vibrations. These findings establish a microscopic framework for understanding the interplay between spin, crystal-field, and lattice degrees of freedom in this multiferroic $4d$-$4f$ compound.