### 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
joypad->probe_joypads();
		} break;
		case WM_DESTROY: {
			Input::get_singleton()->flush_buffered_events();
		} break;
		case WM_SETCURSOR: {
			if (LOWORD(lParam) == HTCLIENT) {
				if (windows[window_id].window_has_focus && (mouse_mode == MOUSE_MODE_HIDDEN || mouse_mode == MOUSE_MODE_CAPTURED || mouse_mode == MOUSE_MODE_CONFINED_HIDDEN)) {
					
					if (hCursor == nullptr) {
						hCursor = SetCursor(nullptr);
					} else {
						SetCursor(nullptr);
					}
				} else {
					if (hCursor != nullptr) {
						CursorShape c = cursor_shape;
						cursor_shape = CURSOR_MAX;
						cursor_set_shape(c);
						hCursor = nullptr;
					}
				}
			}
		} break;
		case WM_DROPFILES: {
			HDROP hDropInfo = (HDROP)wParam;
			const int buffsize = 4096;
			WCHAR buf[buffsize];
			int fcount = DragQueryFileW(hDropInfo, 0xFFFFFFFF, nullptr, 0);
			Vector<String> files;