In this example, the CRISPR system is not used to engineer the phages, but is encoded on the phage genome and targeted at the bacterial genome to more efficiently kill the infected bacteria by destroying the bacterial genome. It is an interesting approach. However, if the phages kill the bacteria before the bacteria can propagate the phages, this may limit the ability of the phages to stay in the system long enough to kill of the bacterial infection.
Are you sure this is true? I recall seeing a documentary a few years back about phage therapy in (some part of) Georgia. According to the documentary, phage therapy was pretty common and widespread there. It didn’t seem like an isolated experiment.