The emission of propagating MHD waves from the boundaries of flow channels that are unstable to the Kelvin-Helmholtz Instability (KHI) in magnetized plasma is investigated. The KHI and MHD wave emission are found to be two competing processes. It is shown that the fastest growing modes of the KHI surface waves do not coincide with efficient wave energy transport away from a velocity shear boundary. MHD wave emission is found to be inefficient when growth rates of KHI surface waves are maximum, which corresponds to the situation where the ambient magnetic field is perpendicular to the flow channel velocity vector. The efficiency of wave emission increases with increasing magnetic field tension, which in Earth's magnetosphere likely dominates along the nightside magnetopause tailward of the terminator, and within earthward Bursty Bulk Flows (BBFs) in the inner plasma sheet. MHD wave emission may also dominate in Supra-Arcade Downflows (SADs) in the solar corona. Our results suggest that efficient emission of propagating MHD waves along BBF and SAD boundaries can potentially explain observations of deceleration and stopping of BBFs and SADs.