We present SNT-GENOME, a constraint-driven genome reorganization framework that operates under a frozen soft-clamp GKSL-C*-Lie dynamics with a \(\Pi_{\mathrm{ORF}}\) disjoint projection invariant. Unlike unconstrained mutation, SNT-GENOME does not maximize ORF count—it minimizes structural degeneracy under mutation. The system exhibits automatic phase-dependent behavior: on dense genomic sequences (conservation regime) it suppresses spurious ORF inflation by 6.7–12.3 disjoint ORFs relative to random mutation while maintaining lower false ORF rates (FOR), and on sparse sequences (expansion regime) it actively installs new coding structure, achieving \(+28.6\%\) disjoint ORF gain on pUC19 (\(p_{\mathrm{boot}}=0.000\)). A density sweep across 10 *E. coli* windows confirms SNT < Random at every window. The IMMUNE architecture resolves two orthogonal failure modes—representation-level inflation via \(\Pi_{\mathrm{ORF}}\) and dynamics-level CPTP violation via frozen soft-clamp—with four documented errors each mapping directly to one design decision. SNT-GENOME is the first application of the SNT operator algebra to DNA-level sequence organization, extending prior SNT work on neural dynamics (C. elegans), digital organism coevolution (SNT-LIFE), and working-memory architectures (SNT-MEM).