One of the advantages of keeping all the auxiliary files next to the source is that version consistency is maintained between these 3rd party libraries and your source code. If you ever need to go back and debug a specific version, you can pull the entire set of source+config and have it all be the same version.
That being said I'd put them in a $project/config/
directory, or some such, rather than in $project/src/java
itself. They're not source, nor java, really, so it's misleading having them in that directory.
When you really get down to it, though, this is an issue of personal style. There's no "Right" answer and you should be talking with those team members and understanding why they made this decision. Using this thread as evidence to support a unilateral decision probably won't go over well. ;)