Extremely late on the answer, and my apologies. Duplicates of existing songs were never outright disallowed, they were just heavily discouraged, partly because we encouraged authors to reach out to one another for collaborating on improvements, and partly because the old database wasn’t really well equipped to handle duplicate songs. As for Clone Hero support, while we did encourage uploading of customs for other platforms, we still required an XBox 360 download also.
With the new database, the second problem has been solved and the 360 requirement has gone away. That means if you’ve authored a song for Clone Hero, and no one else offered a CH custom for that song, you are welcome to upload yours, regardless of whether there is already a custom for Rock Band 3 or any other game. If we do already have a Clone Hero custom for a particular song, we would still encourage reaching out to that author if you think there is room for improvement, but that isn’t required.
Simply put, in almost all cases now, upload away!