Dose-Volume Histograms (DVH) discard spatial information by summarizing 3D distributions into 1D curves. This study quantifies this loss in Gamma Knife radiosurgery and introduces TopoGK, a novel unsupervised deep learning framework capturing full 3D dose geometry. Ninety-six vestibular schwannoma plans were analyzed. Dose grids were tumor-centered, resampled to \({64}^{3}\) voxels, and normalized to \({\text{D}}_{max}\) . A 3D Convolutional Variational Autoencoder compressed each dose-mask volume into a 64dimensional spatial embedding. Spatial information loss was quantified by comparing pairwise DVH and latent distances both globally and within volume-stratified subgroups. Physical validation employed hotspot center-of-mass displacement, gradient anisotropy, and a novel Spatial Discordance Index (SDI). Five-fold cross-validation ensured generalizability. A linear PCA baseline was included for comparison. The correlation between DVH and spatial similarity was weak ( \(=0.132;\text{r}=0.109\) within volume-matched pairs). Among DVH-matched pairs, the hotspot exhibited a median physical displacement of 2.81 mm (90th percentile: 4.69 mm), and 61.8–76.5% exceeded heuristic geometric SDI thresholds. Multivariate regression ( \({\text{R}}^{2}=0.621\) ; volume-adjusted \({\text{R}}^{2}=0.487\) ) confirmed that the learned embedding is driven by spatial metrics-hotspot displacement ( \(\upbeta =0.47\) ) and anisotropy ( \(\upbeta =0.18\) ) rather than DVH ( \(\upbeta =0.10\) ). Held-out reconstruction SSIM reached \(0.943\pm 0.018\) . TopoGK outperformed PCA in spatial correlation ( \({\text{r}}_{\text{C}\text{O}\text{M}}=\) 0.451 vs. 0.287). DVH similarity does not guarantee spatial dose equivalence. The proposed framework provides a physically validated spatial fingerprint capturing geometric variations invisible to conventional plan evaluation. As a proof-of-concept in single-fraction vestibular schwannoma radiosurgery, these results motivate further investigation toward spatially-aware quality assurance in stereotactic radiosurgery.