We, first, attempt to single out the measures of cosmological perturbations that are least afflicted by gauge artifacts and directly connect inhomogeneous large-scale evolution with microscopic kinetics and interactions. We seek perturbation measures (i) whose dynamics is completely specified by the physics within the local Hubble volume and (ii) which are practically applicable on microscopic scales and retain their microscopic physical meaning on all scales in any homogeneous and isotropic geometry. We identify such natural measures for linear perturbations of species' density, and for nonlinear perturbations of phase-space distribution and radiation intensity. When these measures are applied to linear evolution in the Newtonian gauge, the equations acquire an explicit Cauchy structure and nonsingular superhorizon limit, while their solutions simplify. We prove that all measures of linear overdensity that satisfy (i) and (ii) coincide in the superhorizon limit. We then show that, contrary to the prevailing view, the perturbations of the cosmic microwave background (CMB) are not resonantly boosted by their self-gravity at horizon entry in the radiation era. This explains the mildness of the CMB signatures caused by the dark species which may be abundant in the radiation era, e.g. neutrinos or early quintessence. Such species can still be well constrained due to their characteristic nondegenerate signatures on scales l greater than or similar to 200, where the cosmic variance is low. We find, on the other hand, that the dark matter inhomogeneities in the matter era gravitationally suppress large-angle CMB anisotropy by an order of magnitude stronger than previously stated. (In a cosmology dominated by pressureless matter, the suppression of CMB temperature autocorrelation C-l is 25-fold.) Hence, despite the larger cosmic variance at the affected l less than or similar to 200, the CMB anisotropy on these scales is a useful probe of the dark sectors in the matter era.