Different genotypes may compete with each other in a way that is not beneficial for the population. A pure line optimized for a certain environment or usage outperforms the CCP under these specific conditions.
There is no reason to believe that the Darwinian selection will work in the desired direction for  traits such as baking quality. Natural selection and in-field human selection act on the plant stage, not the seed stage.
Common Bunt is a seed borne disease in wheat. In conventional farming it is controlled by fungicide treatment of seeds. In organic farming seeds can be cleaned by brushing before sowing, but it is also desirable that plants have genetic resistance. A CCP, including crosses of resistant cultivars, was grown with heavy common bunt infection for 5 years and it appeared to get more resistant, but the common bunt's virulence appeared to change at least as fast. The overall result was that infection levels went up.