The dummy parent (which is currently onscreen, has override redirect attribute and is invisible only because of shape set on it; see 35193586f78863810f6bb886abca2bc940890acd) normally gets on top of the [fullscreen] rendering window. At least on Gnome / x11 that prevents Vulkan presentation from flipping.
This patch avoids the creation of that dummy parent altogether when it is totally not needed, without introducing any complications (or maybe even arguably with a simplification) for doing that. This is of course not a full solution, there are many cases when dummy parent will be created while the window being presented still could be clipped and it worth looking into finding a way of making that window not preventing the flipping one or another way. But just not creating X window when not needed looks to me like the right thing to do regardless.