We prove existence of a stochastic flow of diffeomorphisms generated by SDEs with drift in $L^q_t C^{0, α}_x$ for any $q \in [2, \infty)$ and $α\in (0, 1)$. This result is achieved using a Zvonkin-type transformation for the SDE. As a key intermediate step, well-posedness and optimal regularity for a class of parabolic PDEs related to the transformation is established. Using the existence of a differentiable stochastic flow, we prove well-posedness of $BV_\text{loc}$-solutions of stochastic transport equations and weak solutions of stochastic continuity equations with so-called transport noise and velocity fields in $L^q_t C^{0, α}_x$. For both equations, solutions may fail to be unique in the deterministic setting.