### 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
_THREAD_SAFE_METHOD_
	ERR_FAIL_COND(!windows.has(p_window));
	ERR_FAIL_COND_MSG(p_window == MAIN_WINDOW_ID, "Main window cannot be deleted.");
	popup_close(p_window);
	WindowData &wd = windows[p_window];
	while (wd.transient_children.size()) {
		window_set_transient(*wd.transient_children.begin(), INVALID_WINDOW_ID);
	}
	if (wd.transient_parent != INVALID_WINDOW_ID) {
		window_set_transient(p_window, INVALID_WINDOW_ID);
	}
#ifdef VULKAN_ENABLED
	if (context_vulkan) {
		context_vulkan->window_destroy(p_window);
	}
#endif
#ifdef GLES3_ENABLED
	if (gl_manager) {
		gl_manager->window_destroy(p_window);
	}
#endif
	if ((tablet_get_current_driver() == "wintab") && wintab_available && windows[p_window].wtctx) {
		wintab_WTClose(windows[p_window].wtctx);
		windows[p_window].wtctx = 0;
	}
	DestroyWindow(windows[p_window].hWnd);
	windows.erase(p_window);
}
void DisplayServerWindows::gl_window_make_current(DisplayServer::WindowID p_window_id) {