We prove that a commutative association scheme is imprimitive if and only if it admits a multivariate $P$- or $Q$-polynomial structure with respect to an elimination-type monomial order. This provides a direct bridge between the classical theory of block and quotient schemes for imprimitive association schemes and elimination theory in computational commutative algebra. For an imprimitive multivariate $P$- or $Q$-polynomial association scheme, we determine the induced multivariate polynomial structures on the quotient and block schemes and describe their associated polynomials via explicit specializations, variable deletions, and rescalings of the original associated polynomials. At the level of zero-dimensional ideals, we show that the ideal of the block scheme is exactly an elimination ideal, whereas the ideal of the quotient scheme is obtained by adjoining the valency relations for the eliminated variables and then eliminating. As applications, we study direct products and crested products from the viewpoint of multivariate polynomiality, and we characterize the schemes that are multivariate $P$- or $Q$-polynomial with respect to every monomial order as precisely the direct products of univariate $P$- or $Q$-polynomial schemes. We also discuss formal duality, composition series, and several related open problems.