What is the reason you need the deployment to be in the deployments folder? If you have a real requirement for it to be in that location then you may be better off with your original plug-in to just make the copy.
The WildFly plug-in that you are using now operates differently, from AS7 it has been possible to remotely connect to the management interfaces of the server and upload a deployment to the server - that is why it is being stored in the data/content folder as the plug-in is uploading it to the server and this is where uploaded content is stored. Secondly the plug-in itself is not writing the standalone.xml content this is being written by the running server after the content has been uploaded.
The reason the deployments folder still exists is so that we can continue to support hot deployment of deployments, however using the management operations as used by the plug-in is really preferable as it makes it possible to easily switch from a local server to a remote server with minimal configuration changes.