### 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
Color early_color;
			if (!_get_window_early_clear_override(early_color)) {
				break;
			}
			bool must_recreate_brush = !window_bkg_brush || window_bkg_brush_color != early_color.to_argb32();
			if (must_recreate_brush) {
				if (window_bkg_brush) {
					DeleteObject(window_bkg_brush);
				}
				window_bkg_brush = CreateSolidBrush(RGB(early_color.get_r8(), early_color.get_g8(), early_color.get_b8()));
			}
			HDC hdc = (HDC)wParam;
			RECT rect = {};
			if (GetUpdateRect(hWnd, &rect, true)) {
				FillRect(hdc, &rect, window_bkg_brush);
			}
			return 1;
		} break;
		case WM_PAINT: {
			Main::force_redraw();
		} break;
		case WM_SETTINGCHANGE: {
			if (lParam && CompareStringOrdinal(reinterpret_cast<LPCWCH>(lParam), -1, L"ImmersiveColorSet", -1, true) == CSTR_EQUAL) {
				if (is_dark_mode_supported() && dark_title_available) {
					BOOL value = is_dark_mode();
					::DwmSetWindowAttribute(windows[window_id].hWnd, DWMWA_USE_IMMERSIVE_DARK_MODE, &value, sizeof(value));
				}
			}
		} break;
		case WM_THEMECHANGED: {