currently, the hierarchy is flattened out, and all the headers files are copied into a single Headers directory, no matter what subfolder they were in, in my Classes folder.
This is a problem when referencing the headers, if the headers have "include" statements that reference other headers in subfolders.
in particular, this screws up BridgeSupport compilation.
My understanding is the Copy Headers behavior always flattens the file structure. You can either add a custom file copy or a custom script at the end of the process that copies (cp -r) the headers from their original location to your desired destination. These are viable workarounds for now. Meanwhile, definitely post your request to bugreport.apple.com.