### 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)
button_create->set_toggle_mode(true);
	button_create->set_button_group(tools_button_group);
	button_create->set_pressed(true);
	button_create->set_tooltip_text(TTR("Add polygon tool"));
	toolbar->add_child(button_create);
	button_edit = memnew(Button);
	button_edit->set_theme_type_variation("FlatButton");
	button_edit->set_toggle_mode(true);
	button_edit->set_button_group(tools_button_group);
	button_edit->set_tooltip_text(TTR("Edit points tool"));
	toolbar->add_child(button_edit);
	button_delete = memnew(Button);
	button_delete->set_theme_type_variation("FlatButton");
	button_delete->set_toggle_mode(true);
	button_delete->set_button_group(tools_button_group);
	button_delete->set_tooltip_text(TTR("Delete points tool"));
	toolbar->add_child(button_delete);
	button_advanced_menu = memnew(MenuButton);
	button_advanced_menu->set_flat(false);
	button_advanced_menu->set_theme_type_variation("FlatMenuButton");
	button_advanced_menu->set_toggle_mode(true);
	button_advanced_menu->get_popup()->add_item(TTR("Reset to default tile shape"), RESET_TO_DEFAULT_TILE, Key::F);
	button_advanced_menu->get_popup()->add_item(TTR("Clear"), CLEAR_TILE, Key::C);
	button_advanced_menu->get_popup()->add_separator();
	button_advanced_menu->get_popup()->add_item(TTR("Rotate Right"), ROTATE_RIGHT, Key::R);
	button_advanced_menu->get_popup()->add_item(TTR("Rotate Left"), ROTATE_LEFT, Key::E);
	button_advanced_menu->get_popup()->add_item(TTR("Flip Horizontally"), FLIP_HORIZONTALLY, Key::H);
	button_advanced_menu->get_popup()->add_item(TTR("Flip Vertically"), FLIP_VERTICALLY, Key::V);
	button_advanced_menu->get_popup()->connect("id_pressed", callable_mp(this, &GenericTilePolygonEditor::_advanced_menu_item_pressed));
	button_advanced_menu->set_focus_mode(FOCUS_ALL);