### 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)
ERR_FAIL_COND_V(!tile_set.is_valid(), nullptr);
	ERR_FAIL_COND_V(!tile_set->has_source(p_cell.source_id), nullptr);
	TileData *td = nullptr;
	TileSetSource *source = *tile_set->get_source(p_cell.source_id);
	TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
	if (atlas_source) {
		ERR_FAIL_COND_V(!atlas_source->has_tile(p_cell.get_atlas_coords()), nullptr);
		ERR_FAIL_COND_V(!atlas_source->has_alternative_tile(p_cell.get_atlas_coords(), p_cell.alternative_tile), nullptr);
		td = atlas_source->get_tile_data(p_cell.get_atlas_coords(), p_cell.alternative_tile);
	}
	return td;
}
void TileDataEditor::_bind_methods() {
	ClassDB::bind_method(D_METHOD("_tile_set_changed_deferred_update"), &TileDataEditor::_tile_set_changed_deferred_update);
	ADD_SIGNAL(MethodInfo("needs_redraw"));
}
void TileDataEditor::set_tile_set(Ref<TileSet> p_tile_set) {
	if (tile_set.is_valid()) {
		tile_set->disconnect_changed(callable_mp(this, &TileDataEditor::_tile_set_changed_plan_update));
	}
	tile_set = p_tile_set;
	if (tile_set.is_valid()) {
		tile_set->connect_changed(callable_mp(this, &TileDataEditor::_tile_set_changed_plan_update));
	}
	_tile_set_changed_plan_update();
}
bool DummyObject::_set(const StringName &p_name, const Variant &p_value) {