The deployment items list is a Visual Studio feature, not a Test Studio feature. Thus it's under total control of Microsoft. Also I'm afraid that's just the way it works in Visual Studio. It will always flatten any folder structures during the initialization phase of test execution as it creates the Out folder with the artifacts to test.
To do it differently you'll need to write your own coded step to create/copy the files into the folder structure you desire for your test run.
the Telerik team