This study introduces a dual-matrix computational architecture to mathematically quantify the morphological and theological divergence of 196 Hindu and Vajrayana Buddhist esoteric deities. Physical morphology is evaluated via a discrete Gower distance matrix enhanced by a novel "Cardinality Weighting" algorithm, while theological function is mapped via dense vector embeddings generated from Large Language Model (LLM) semantic expansions, explicitly utilized as a synthetic proxy to mitigate circular reasoning. The multi-modal topological projections provide algorithmic validation of "iconographic camouflage", demonstrating how distinct visual forms structurally obscure shared cross-tradition functions. Furthermore, I computationally model the "Atin Effect" - serving simultaneously as a psychological observation of sequential cognitive bias and a machine learning benchmark - demonstrating how high-cardinality esoteric anchors (e.g., a veena or a severed head) override systemic theological disparities to mathematically cluster orthodox and Tantric entities. Cross-tradition spatial analysis establishes that the highest esoteric manifestations, such as the Hindu Chinnamasta and the Buddhist Chinnamunda, share a near-identical mathematical coordinate across both visual (
DG=0.288) and semantic (
DC=0.068) boundaries, indicating a 1:1 esoteric transfer. By open-sourcing this architecture, I provide a scalable, unsupervised machine learning tool for Digital Humanities scholars and comparative theologians to rigorously map latent structural continuities across qualitative cultural corpora.