### 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 (pInputs) {
				if (GetTouchInputInfo((HTOUCHINPUT)lParam, cInputs, pInputs, sizeof(TOUCHINPUT))) {
					for (UINT i = 0; i < cInputs; i++) {
						TOUCHINPUT ti = pInputs[i];
						POINT touch_pos = {
							TOUCH_COORD_TO_PIXEL(ti.x),
							TOUCH_COORD_TO_PIXEL(ti.y),
						};
						ScreenToClient(hWnd, &touch_pos);
						
						if (ti.dwFlags & TOUCHEVENTF_MOVE) {
							_drag_event(window_id, touch_pos.x, touch_pos.y, ti.dwID);
						} else if (ti.dwFlags & (TOUCHEVENTF_UP | TOUCHEVENTF_DOWN)) {
							_touch_event(window_id, ti.dwFlags & TOUCHEVENTF_DOWN, touch_pos.x, touch_pos.y, ti.dwID);
						}
					}
					bHandled = TRUE;
				} else {
					
				}
				memdelete_arr(pInputs);
			} else {
				
			}
			if (bHandled) {
				CloseTouchInputHandle((HTOUCHINPUT)lParam);
				return 0;
			}
		} break;
		case WM_DEVICECHANGE: {