The THz spectrum of density fluctuations, S(Q, ω), of vitreous GeO2 at ambient temperature was measured by inelastic x-ray scattering from ambient pressure up to pressures well beyond that of the known α-quartz to rutile polyamorphic (PA) transition. We observe significant differences in the spectral shape measured below and above the PA transition, in particular, in the 30-80 meV range. Guided by first-principle lattice dynamics calculations, we interpret the changes in the phonon dispersion as the evolution from a quartz-like to a rutile-like coordination. Notably, such a crossover is accompanied by a cusp-like behavior in the pressure dependence of the elastic response of the system. Overall, the presented results highlight the complex fingerprint of PA phenomena on the high-frequency phonon dispersion.