Under the framework of unified time scale, phase--spectral shift--density of states chain, and boundary time geometry, we provide a spectral windowing unified formulation for the cosmological constant and dark energy, implementing a discretized version in Matrix Universe and Quantum Cellular Automaton (QCA) Universe. First, on even-dimensional asymptotically hyperbolic or conformally compact geometries and static patch de Sitter backgrounds satisfying relative trace class and good scattering assumptions, we utilize Birman--Krein and Lifshits--Krein trace formulas to unify generalized scattering phase derivative, spectral shift function derivative, and relative density of states (DOS) in frequency variable into a scale density \kappa(\omega)=\varphi'(\omega)/\pi=\Delta\rho_\omega(\omega)=(2\pi)^{-1}tr Q(\omega), where Q(\omega) is the Wigner--Smith group delay matrix. Provided the logarithmic frequency window kernel satisfies Mellin vanishing conditions, we establish a windowed Tauberian theorem: the finite part of the small-s heat kernel difference is equivalent to the logarithmic window average of \Theta'(\omega) at scale \mu\sim s^{-1/2}, thereby completely rewriting vacuum energy density renormalization as a windowed integral of \kappa(\omega). Second, in the Matrix Universe representation, viewing FRW and de Sitter universes as scattering backgrounds containing horizon channels, we construct the cosmological scattering matrix S_{cos}(\omega) and its scale density \kappa_{cos}(\omega) and window kernel \Xi_{cos}(\omega), proving that the effective cosmological constant increment \Lambda_{eff}(\mu)-\Lambda_{eff}(\mu_0) can be expressed as the logarithmic frequency windowed spectral integral of the DOS difference between ``Physical Universe'' and ``Reference Universe'', thus reducing the cosmological constant problem to a relative spectral problem under unified time scale. Third, within the Universe QCA object \mathfrak U_{QCA}=(\Lambda,\mathcal H_{cell},\mathcal A,\alpha,\omega_0), replacing continuous spectrum \omega with quasi-energy spectrum \varepsilon_j(k), we define the relative band density \Delta\rho_j(k) of QCA Universe and Reference QCA, constructing the discrete windowed formula \Lambda_{eff}(\mu)=\sum_j\int_{BZ}\mathcal W_\mu(\varepsilon_j(k))\,\Delta\rho_j(k)\,d^dk. Under conditions where high-energy bands satisfy symmetric pairing and inter-band harmonious sum rules, we prove that contributions to \Lambda_{eff} from high-energy regions are exponentially or power-law suppressed after windowing, leaving only finite residuals contributed by low-energy mass thresholds and topological modes within the redshift window, yielding a natural suppression estimate \Lambda_{eff}\sim m_{IR}^4(m_{IR}/M_{UV})^{\gamma} with \gamma>0. Finally, interfacing the spectral windowing--band structure mechanism with running vacuum models in curved spacetime QFT, we construct the dark energy equivalent equation of state w_{de}(z)\approx -1+\delta w(z) within the unified time scale framework, where \delta w(z) is controlled by the slow evolution of \Xi(\omega) in the corresponding frequency band, compatible with current observational constraints of ``overall close to w=-1 allowing small amplitude evolution''. Overall, this paper restates ``why the cosmological constant is far smaller than M_{Pl}^4'' as ``what kind of windowed sum rule the relative DOS satisfies under unified time scale'', providing a self-consistent spectral theoretical framework for discussing the magnitude and running behavior of dark energy uniformly within Matrix Universe and QCA Universe. The cosmological constant problem is thus embedded into the broader program of unified time scale--scattering--discrete universe.