This problem is still there. More specifically, when unpacking tar.gz on linux, and the files have specific permissions for the group in the archive, they are incorrect after the unpack.
I believe, the reason is that java.io.File class does not support Posix style permissions, and obviously this is what is used in the dependency plugin.
There are two ways of fixing it.
First way is to use java.nio.file.attribute package that supports Posix permissions, but this is available only since Java 7, and so this fix will not work with Java 6. I personally would prefer this solution; we all will start using Java 7 anyway at some point.
Another way is to call tar utility from inside the plugin, instead of pure clean Java solution.