### Godot version

4.0.beta12

### System information

Windows 11, RTX 3080

### Issue description

When a Window Node is created with it's Transparent flag set to true and Project Settings --> Display --> Window --> Subwindows --> Embed Subwindows is false, the Window has a black background. By cycling the transparent flag from false and back to true again, during runtime, the window's background then becomes transparent. 

### Steps to reproduce

Attempt to create a Non-embedded Subwindow with a transparent background using the appropriate flags. 

### Minimal reproduction project

Note: this project is from Reddit user [gongpha](https://www.reddit.com/user/gongpha/) and his Reddit post [Learning a Godot 4.0 Window node](https://www.reddit.com/r/godot/comments/xr8yxn/learning_a_godot_40_window_node/)

https://github.com/gongpha/godot4-window-test
wc.lpszClassName = L"Engine";
	if (!RegisterClassExW(&wc)) {
		MessageBox(nullptr, "Failed To Register The Window Class.", "ERROR", MB_OK | MB_ICONEXCLAMATION);
		r_error = ERR_UNAVAILABLE;
		return;
	}
	_register_raw_input_devices(INVALID_WINDOW_ID);
#if defined(VULKAN_ENABLED)
	if (rendering_driver == "vulkan") {
		context_vulkan = memnew(VulkanContextWindows);
		if (context_vulkan->initialize() != OK) {
			memdelete(context_vulkan);
			context_vulkan = nullptr;
			r_error = ERR_UNAVAILABLE;
			return;
		}
	}
#endif
	
#if defined(GLES3_ENABLED)
	if (rendering_driver == "opengl3") {
		GLManager_Windows::ContextType opengl_api_type = GLManager_Windows::GLES_3_0_COMPATIBLE;
		gl_manager = memnew(GLManager_Windows(opengl_api_type));
		if (gl_manager->initialize() != OK) {
			memdelete(gl_manager);
			gl_manager = nullptr;
			r_error = ERR_UNAVAILABLE;
			return;
		}
		RasterizerGLES3::make_current();