I’m not that familiar with the transparency code but I believe the whole window transparency via _NET_WM_WINDOW_OPACITY and GLFW_TRANSPARENT_FRAMEBUFFER option which controls the use of the framebuffers alpha component to determine the window content transparency are different things.
Documentation for Window transparency covers the basics, including glfwSetWindowOpacity which like _NET_WM_WINDOW_OPACITY sets the entire Windows transparency.
On X11 I believe GLFW_TRANSPARENT_FRAMEBUFFER requires a compositing window manager and support for an alphaMask.
So it is possible your system does not support frame buffer transparency, but does support full window transparency.
I don’t use Ubuntu, but I don’t think it matters, really. It’s all about the window manager.
Xfwm (the window manager for the Xfce environment) supports transparency, and GLFW creates transparent windows without any problem. On the other hand, simple stacking window managers such as Openbox will ignore whatever opacity you set with glfwSetWindowOpacity. Same for tiling window managers such as Stumpwm.