### 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 (!Main::is_iterating()) {
					Main::iteration();
				}
			} else if (wParam == windows[window_id].focus_timer_id) {
				_process_activate_event(window_id, windows[window_id].saved_wparam, windows[window_id].saved_lparam);
				KillTimer(windows[window_id].hWnd, wParam);
				windows[window_id].focus_timer_id = 0U;
			}
		} break;
		case WM_SYSKEYDOWN:
		case WM_SYSKEYUP:
		case WM_KEYUP:
		case WM_KEYDOWN: {
			if (wParam == VK_SHIFT) {
				shift_mem = (uMsg == WM_KEYDOWN || uMsg == WM_SYSKEYDOWN);
			}
			if (wParam == VK_CONTROL) {
				control_mem = (uMsg == WM_KEYDOWN || uMsg == WM_SYSKEYDOWN);
			}
			if (wParam == VK_MENU) {
				alt_mem = (uMsg == WM_KEYDOWN || uMsg == WM_SYSKEYDOWN);
				if (lParam & (1 << 24)) {
					gr_mem = alt_mem;
				}
			}
			if (mouse_mode == MOUSE_MODE_CAPTURED) {
				
				if (wParam == VK_F4 && alt_mem && (uMsg == WM_KEYDOWN || uMsg == WM_SYSKEYDOWN)) {
					_send_window_event(windows[window_id], WINDOW_EVENT_CLOSE_REQUEST);
				}