### 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
uint32_t pointer_id = LOWORD(wParam);
			POINTER_INPUT_TYPE pointer_type = PT_POINTER;
			if (!win8p_GetPointerType(pointer_id, &pointer_type)) {
				break;
			}
			if (pointer_type != PT_PEN) {
				break;
			}
			windows[window_id].block_mm = true;
			return 0;
		} break;
		case WM_POINTERLEAVE: {
			windows[window_id].block_mm = false;
			return 0;
		} break;
		case WM_POINTERUPDATE: {
			if (mouse_mode == MOUSE_MODE_CAPTURED && use_raw_input) {
				break;
			}
			if ((tablet_get_current_driver() != "winink") || !winink_available) {
				break;
			}
			uint32_t pointer_id = LOWORD(wParam);
			POINTER_INPUT_TYPE pointer_type = PT_POINTER;
			if (!win8p_GetPointerType(pointer_id, &pointer_type)) {
				break;
			}
			if (pointer_type != PT_PEN) {
				break;
			}