Motile and driven particles confined in microfluidic channels exhibit interesting emergent behavior, from propagating density bands to density shock waves. A deeper understanding of the physical mechanisms responsible for these emergent structures is relevant to a number of physical and biomedical applications. Here, we study the formation of density shock waves in the context of an idealized model of microswimmers confined in a narrow channel and subject to a uniform external flow. Interestingly, these density shock waves exhibit a transition from "subsonic" with compression at the back to "supersonic" with compression at the front of the population as the intensity of the external flow increases. This behavior is the result of a nontrivial interplay between hydrodynamic interactions and geometric confinement, and it is confirmed by a novel quasilinear wave model that properly captures the dependence of the shock formation on the external flow. These findings can be used to guide the development of novel mechanisms for controlling the emergent density distribution and the average population speed, with potentially profound implications on various processes in industry and biotechnology, such as the transport and sorting of cells in flow channels.