### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
base_control->set_clip_contents(true);
	base_control->set_focus_mode(Control::FOCUS_CLICK);
	root->add_child(base_control);
	snap_subdivision->connect("value_changed", callable_mp((CanvasItem *)base_control, &CanvasItem::queue_redraw).unbind(1));
	snap_subdivision->connect("value_changed", callable_mp(this, &GenericTilePolygonEditor::_store_snap_options).unbind(1));
	editor_zoom_widget = memnew(EditorZoomWidget);
	editor_zoom_widget->setup_zoom_limits(0.125, 128.0);
	editor_zoom_widget->set_position(Vector2(5, 5));
	editor_zoom_widget->connect("zoom_changed", callable_mp(this, &GenericTilePolygonEditor::_zoom_changed).unbind(1));
	editor_zoom_widget->set_shortcut_context(this);
	root->add_child(editor_zoom_widget);
	button_center_view = memnew(Button);
	button_center_view->set_anchors_and_offsets_preset(Control::PRESET_TOP_RIGHT, Control::PRESET_MODE_MINSIZE, 5);
	button_center_view->connect("pressed", callable_mp(this, &GenericTilePolygonEditor::_center_view));
	button_center_view->set_theme_type_variation("FlatButton");
	button_center_view->set_disabled(true);
	root->add_child(button_center_view);
	snap_subdivision->set_value_no_signal(EditorSettings::get_singleton()->get_project_metadata("editor_metadata", "tile_snap_subdiv", 4));
	_set_snap_option(EditorSettings::get_singleton()->get_project_metadata("editor_metadata", "tile_snap_option", SNAP_NONE));
}
void TileDataDefaultEditor::_property_value_changed(StringName p_property, Variant p_value, StringName p_field) {
	ERR_FAIL_NULL(dummy_object);
	dummy_object->set(p_property, p_value);
	emit_signal(SNAME("needs_redraw"));
}
Variant TileDataDefaultEditor::_get_painted_value() {
	ERR_FAIL_NULL_V(dummy_object, Variant());
	return dummy_object->get(property);
}
void TileDataDefaultEditor::_set_painted_value(TileSetAtlasSource *p_tile_set_atlas_source, Vector2 p_coords, int p_alternative_tile) {