While motivated by structural problems in mathematical music theory, this article introduces a novel combinatorial framework that advances the classification of cyclic cubic bipartite graphs. We extend the classical study of Levi graphs by endowing their vertices with an internal algebraic anatomy -- specifically, treating them not as empty geometric nodes, but as defined subsets of a cyclic base space Z_n. This internal structure allows us to formalize and classify a highly restricted class of graph isomorphisms: those strictly induced by global affine bijections f(x) = ax+b (mod n) operating directly on the underlying base set. By applying this framework to generalized tone networks (Tonnetze) unrolled via the Chinese Remainder Theorem in composite dimensions -- specifically the classic 12-TET (3x4) and the decaphonic 10-TET (2x5) -- we reveal absolute geometric anchors for these spaces, namely the (9,4) and (6,5) systems respectively. We completely classify the topological orbits of these structured graphs, proving a fundamental architectural dichotomy: while the isomorphic landscape of 12-TET splits into an orientation-preserving family and an orientation-reversing chiral mirror (providing a rigorous foundation for musical Negative Harmony), the 10-TET space is unconditionally orientation-preserving. Finally, we demonstrate that these abstract combinatorial properties manifest as rigidly coherent, parallel auditory universes through explicit structural voice-leading maps and acoustic physical modeling synthesis.