### 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
if (context_vulkan) {
			if (context_vulkan->window_create(id, p_vsync_mode, wd.hWnd, hInstance, WindowRect.right - WindowRect.left, WindowRect.bottom - WindowRect.top) != OK) {
				memdelete(context_vulkan);
				context_vulkan = nullptr;
				windows.erase(id);
				ERR_FAIL_V_MSG(INVALID_WINDOW_ID, "Failed to create Vulkan Window.");
			}
			wd.context_created = true;
		}
#endif
#ifdef GLES3_ENABLED
		if (gl_manager) {
			if (gl_manager->window_create(id, wd.hWnd, hInstance, WindowRect.right - WindowRect.left, WindowRect.bottom - WindowRect.top) != OK) {
				memdelete(gl_manager);
				gl_manager = nullptr;
				windows.erase(id);
				ERR_FAIL_V_MSG(INVALID_WINDOW_ID, "Failed to create an OpenGL window.");
			}
			window_set_vsync_mode(p_vsync_mode, id);
		}
#endif
		RegisterTouchWindow(wd.hWnd, 0);
		DragAcceptFiles(wd.hWnd, true);
		if ((tablet_get_current_driver() == "wintab") && wintab_available) {
			wintab_WTInfo(WTI_DEFSYSCTX, 0, &wd.wtlc);
			wd.wtlc.lcOptions |= CXO_MESSAGES;
			wd.wtlc.lcPktData = PK_STATUS | PK_NORMAL_PRESSURE | PK_TANGENT_PRESSURE | PK_ORIENTATION;
			wd.wtlc.lcMoveMask = PK_STATUS | PK_NORMAL_PRESSURE | PK_TANGENT_PRESSURE;
			wd.wtlc.lcPktMode = 0;
			wd.wtlc.lcOutOrgX = 0;