Charts in FMP13 with transparent backgrounds paste or drag-drop into many programs (FMP itself, Keynote, Numbers, many others) with a white background. I don't think this is entirely FileMaker's fault since some programs like GraphicConverter and Preview will open them (New from Clipboard) with their transparency intact.
But, with WebDirect charts will drag-drop into the programs I have tested and maintain their transparent backgrounds.
For simple transfer of a chart with transparency, WebDirect is better suited than FMP. Not sure what happens within Windows.