The first thing I want you to know is that I don’t know OpenGL (temporary situation ;D), so the things I’m writing may be incorrect.
I did some experiments with Java3D and OpenGL (JOGL) on win. Just simple things. I ever wanted to draw something on a buffer and then grab the resulting pixels and save them as TGA with transparent background.
No way. I always got a fully opaque black background.
I did some investigation in order to get a transparent background. I posted almost everywhere without getting any convincing solution. Someone told me that I was initializing OpenGL in the wrong way. Some other suggested to chroma-key the background (UGLY! say goodbye to speed and antialiasing).
Now I am almost certain that the reason is the implementation of OpenGL on windows: ChoosePixelFormat does not give any background transparence, even if requested. Maybe It’s a fault of the Microsoft OpenGL implementation. I don’t know.
Now, talking about Java2D on win, I suspect it will be unlikely it will be implemented on top of OpenGL for the reasons above, at least without breaking backwards compatibility with the existing Java2D graphics software.