Rad Controls for Silverlight Q2 2009 SP1 is indeed official and it is built agains SL3.
This link will take you to the download page of Q2 2009 SP1 - http://www.telerik.com/account/downloads/product-versions/single-version.aspx?pmvid=2079
Once you open the page you should be able to download the installer or the just the binaries. SP1 could be identified by the version 2009.2 812.
We have moved the design assemblies to another folder so that they do not clutter the root binary folder.
We will check the discrepancies in the folder structures that you have mentioned and fix them as soon as possible. Thank you for reporting that.
the Telerik team