These wouldn't be Win32 subwindows as X11 child windows (as I heard Wine doesn't do), but rather, a child window of the main window used solely for showing OpenGL on. I can't, in my admittedly limited knowledge, think of why it wouldn't work, and it should also help clear the problem Wine has with Win32 child windows using OpenGL since they'd implicitly clip to the child window extents, instead of trying to hack the scissors test. The X11 child window for OpenGL would be completely transparent to the app (as in, opengl wouldn't announce its existance, and the rest of the code wouldn't care about it).
Just wondered what would happen in the case of a non-X11 child window partially overlapping an X11 OpenGL window? I guess this wouldn't work still even with this solution. This could happen quite easily in an MDI situation.
Mark