Guino just added support for the more plugins / visualizations to be able to be made transparent. As long as they are not DirectX based, and the Milkdrop plugin, is directX based.
As far as an AVS spectrum analyzer and having it embed, you can download my skin, and in the skins/helper files, there are 5 different spectrum analyzers in different colors. You can use these in your skin, or any other skin. Just copy them to your AVS plugins folder.
Skin Download Link