When flattenMode is set to bom the plugin keeps the properties and dependencyManagement sections of the POM. But as of version 1.5.0 it removes the pluginManagement section in bom mode. I believe the behavior of bom mode should be changed to keep the pluginManagement section as well, since it is very similar to dependencyManagement and serves a very similar purpose. See https://www.baeldung.com/maven-plugin-management#plugin-management.