The multiscale hybrid-mixed (MHM) method for the Stokes operator was formally introduced in [R. Araya et al., Comput. Methods Appl. Mech. Engrg., 324, pp. 29–53, 2017] and numerically validated. The method has face degrees of freedom associated with multiscale basis functions computed from local Neumann problems driven by discontinuous polynomial spaces on skeletal meshes. The two-level MHM version approximates the multiscale basis using a stabilized finite element method. This work proposes the first numerical analysis for the one- and two-level MHM method applied to the Stokes/Brinkman equations within a new abstract framework relating MHM methods to discrete primal hybrid formulations. As a result, we generalize the two-level MHM method to include general second-level solvers and continuous polynomial interpolation on faces and establish abstract conditions to have those methods well-posed and optimally convergent on natural norms. We apply the abstract setting to analyze the MHM methods using stabilized and stable finite element methods as second-level solvers with (dis)continuous interpolation on faces. Also, we find that the discrete velocity and pressure variables preserve the balance of forces and conservation of mass at the element level. Numerical benchmarks assess theoretical results.