Industrial point cloud segmentation for Digital Twin construction faces a persistent challenge: safety-critical components such as reducers and valves are systematically misclassified. These failures stem from two compounding factors: such components are rare in training data, yet they share identical local geometry with dominant structures like pipes. This work identifies a dual crisis unique to industrial 3D data extreme class imbalance 215:1 ratio compounded by geometric ambiguity where most tail classes share cylindrical primitives with head classes. Existing frequency-based re-weighting methods address statistical imbalance but cannot resolve geometric ambiguity. We propose spatial context constraints that leverage neighborhood prediction consistency to disambiguate locally similar structures. Our approach extends the Class-Balanced (CB) Loss framework with two architecture-agnostic mechanisms: (1) Boundary-CB, an entropy-based constraint that emphasizes ambiguous boundaries, and (2) Density-CB, a density-based constraint that compensates for scan-dependent variations. Both integrate as plug-and-play modules without network modifications, requiring only loss function replacement. On the Industrial3D dataset (610M points from water treatment facilities), our method achieves 55.74% mIoU with 21.7% relative improvement on tail-class performance (29.59% vs. 24.32% baseline) while preserving head-class accuracy (88.14%). Components with primitive-sharing ambiguity show dramatic gains: reducer improves from 0% to 21.12% IoU; valve improves by 24.3% relative. This resolves geometric ambiguity without the typical head-tail trade-off, enabling reliable identification of safety-critical components for automated knowledge extraction in Digital Twin applications.