Version 2 refines and extends the structural interpretation presented in V1. Additions include an explicit variance–entropy correspondence, boundary–bulk visualization, and a clearer positioning of the work as an interpretative structural bridge rather than a formal proof. This paper proposes a structural reinterpretation of the classical Hilbert–Pólya conjecture within the framework of Generalized Universe Holography (GUH). Rather than postulating the existence of a self-adjoint operator whose spectrum reproduces the nontrivial zeros of the Riemann zeta function, self-adjointness is interpreted as an emergent consequence of boundary completeness and minimal-entropy encoding. Building on recent variance-based reductions of the Riemann Hypothesis, off-critical zeros are interpreted as transverse spectral defects that generate super-quadratic variance growth and entropy excess. Boundary completeness enforces spectral rigidity, naturally confining the spectrum to the critical line. In this setting, the Hilbert–Pólya operator arises as an emergent boundary operator whose real spectrum is structurally enforced rather than axiomatically assumed. Random matrix universality is reinterpreted as describing allowed boundary-aligned fluctuations under minimal-entropy constraints, rather than evidence for a specific microscopic Hamiltonian. This work does not claim a formal proof of the Riemann Hypothesis. Instead, it provides an interpretative structural bridge between analytic number theory, operator theory, and holographic principles, suggesting that arithmetic spectra reflect deeper informational constraints governing emergent mathematical and physical structures.