As noted in an earlier Tip of the Day, typically you do not want a windowless Silverlight control, as there is a high performance price in rendering windowless controls.
However, if you wish to set the background to be transparent, you must remember to set the isWindowless property to true, or the entire Silverlight control will be rendered as solid black.
Both of these properties are set in createObjectEx in default.html.js,
Silverlight.createObjectEx({ source: 'Scene.xaml', parentElement: document.getElementById('SilverlightPlugInHost'), id: 'SilverlightPlugIn', properties: { width: '200', height: '200', background:'transparent', isWindowless: 'true', version: '1.0' },
By setting the Silverlight control as shown, and then adding a rectangle to your XAML with no fill color, you can see that the Silverlight control is transparent,
If however you return to the declaration of the Silverlight control, and change only the isWindowless parameter to false, the entire control is rendered in solid black