The mechanism at work under Wayland with the V3 patch is as follows: a GL window which is now fully transparent is composited above its parent, non-GL window which is fully opaque. What is not colored by GL therefore lets what is behind it appear. Overall, the background color of the parent window is visible in the non-colored parts of the GL scene. That explains why "the background is dark gray instead of being black": that's because the parent window has FLTK's default background color, grey. To get it black, just add a solid black FL_FLAT_BOX Fl_Box to the parent window where the GL subwindow is placed.

I've run your modified shape program and see that the output png-with-transparency file is correct.

In my view, this issue is solved with the one-line V3 patch. It's just necessary, when creating an FL_ALPHA GL scene in an Fl_Gl_Window subwindow to take care of the color of the parent window of this subwindow.

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