Decoherence in superconducting qubits arises from both multilevel dynamics and structured environmental noise, yet perturbative models cannot capture all resulting signatures. Here, EmuPlat couples instruction-set-architecture-level waveform generation to the hierarchical equations of motion HEOM under 1/f non-Markovian pure dephasing. In the resulting non-perturbative regime – where filter-function predictions become quantitatively uninformative – CPMG scaling of a three-level superconducting transmon yields one calibration result, two physical findings, and one structural null. Y-CPMG exhibits axis-dependent scaling-law breakdown – non-monotonic decoherence, partial coherence revival, and pronounced X–Y population asymmetry (0.204 vs < 0.01) – driven by third-level anharmonicity amplified by bath memory; X-CPMG maintains well-behaved power-law scaling with a finite-n transient excess consistent with non-Markovian bath-memory effects. This null result is equally informative: waveform-level differences – Standard versus VPPU realisations – remain undetectable across all coupling strengths. This shows that rotating-frame pure-dephasing coupling renders control-layer detail invisible to scaling observables. These findings define testable predictions, the most experimentally accessible requiring only qualitative verification.