This paper improves guaranteed error control for the Stokes problem with a focus on pressure-robustness, i.e. for discretisations that compute a discrete velocity that is independent of the exact pressure. A Prager-Synge type result relates the errors of divergence-free primal and H(div)-conforming dual mixed methods (for the velocity gradient) with an equilibration constraint that needs special care when discretised. To relax the constraints on the primal and dual method, a more general result is derived that enables the use of a recently developed mass conserving mixed stress discretisation to design equilibrated fluxes that yield pressure-independent guaranteed upper bounds for any pressure-robust (but not necessarily divergence-free) primal discretisation. Moreover, a provably efficient local design of the equilibrated fluxes is presented that reduces the numerical costs of the error estimator. All theoretical findings are verified by numerical examples which also show that the efficiency indices of our novel guaranteed upper bounds for the velocity error are close to 1.