Deployment structure files are top level only. i.e. If you are deploying an .war within a .ear, then the jboss-deployment-structure.xml within the .ear/META-INF/ is what matters.
In an ear the exclusion only applies to ear/lib. To configure it for subdeployments within the .ear, you'll need a sub-deployment element within the .ear/META-INF/jboss-deployment-structure.xml. Here's an example on how the subdeployments can be configured https://docs.jboss.org/author/display/AS7/Class+Loading+in+AS7.
The reason you both see different results is because the application that you mention are packaged differently.