Rapid, high-fidelity analysis of four-dimensional scanning transmission electron microscopy (4D-STEM) datasets from heterogeneous materials remains challenging because coexisting phases, orientation variants, local strain gradients, and intrinsic TEM thin-foil effects produce complex, overlapping diffraction signatures. Here, we present a machine-learning (ML) framework that combines physics-informed geometric descriptors with weighted high-dimensional embeddings to identify latent structural patterns with minimal prior knowledge. By constructing a regularized descriptor space before embedding and density-based clustering, the method improves cluster stability, suppresses noise-driven fragmentation, and reduces sensitivity to embedding hyperparameters. Spatial weighting produced the largest stability gain, increasing median cluster persistence from 0.04 to 0.55 while reducing the noise fraction from approximately 22% to 0%. Rotation weighting increased DBCV from 0.80 to 0.92, although the noise fraction rose from 0.2% to 1.0%, highlighting a trade-off between improved density separation and noise rejection. We validate the framework on two benchmark systems: Si/Si$_x$Ge$_{1-x}$ epitaxial layers with continuous lattice variation and deformation, and multiphase Ti-Nb alloys containing distinct phases and orientation variants. Comparisons with a pretrained vanilla autoencoder and model-free pattern vectorization show that the physics-informed geometric descriptor provides higher cluster fidelity, greater interpretability, and substantially lower dimensionality.

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