The solution to your problem is putting your XML configuration files in the userlib directory. The contents of this directory are copied to the deployment directory (and thus placed in deployment archives). Also, this directory is on the classpath, so you should be able to resolve the XML files.
Could be something that wasn't foreseen yeah, I'd make a ticket for it. I guess you should be given the choice to include non-java files in the javasource folder when making a deployment archive.
As a workaround you can manually add them though, since it's just a zip file. Though if you're doing the deployment yourself you might as well put them in the right place.