I would say a lot of people with Web experience prior to angular, are use to deploying their web artifacts inside a war (i.e. jquery and html inside a Java/Spring project). I ended up doing this to get around CORS issue, after attempting to keep my angular and REST projects separate.
My solution was to move all angular (4) contents, generated with CLI, from my-app to MyJavaApplication/angular. Then I modifed my Maven build to use maven-resources-plugin to move the contents from /angular/dist to the root of my distribution (i.e. $project.build.directory}/MyJavaApplication). Angular loads resources from root of the war by default.
When I started to add routing to my angular project, I further modifed maven build to copy index.html from /dist to WEB-INF/app. And, added a Java controller that redirects all server side rest calls to index.