### 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_MSG(!tiles.has(p_atlas_coords), TileSetSource::INVALID_TILE_ALTERNATIVE, vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	ERR_FAIL_COND_V_MSG(p_alternative_id_override >= 0 && tiles[p_atlas_coords].alternatives.has(p_alternative_id_override), TileSetSource::INVALID_TILE_ALTERNATIVE, vformat("Cannot create alternative tile. Another alternative exists with id %d.", p_alternative_id_override));
	int new_alternative_id = p_alternative_id_override >= 0 ? p_alternative_id_override : tiles[p_atlas_coords].next_alternative_id;
	tiles[p_atlas_coords].alternatives[new_alternative_id] = memnew(TileData);
	tiles[p_atlas_coords].alternatives[new_alternative_id]->set_tile_set(tile_set);
	tiles[p_atlas_coords].alternatives[new_alternative_id]->set_allow_transform(true);
	tiles[p_atlas_coords].alternatives[new_alternative_id]->connect("changed", callable_mp((Resource *)this, &TileSetAtlasSource::emit_changed));
	tiles[p_atlas_coords].alternatives[new_alternative_id]->notify_property_list_changed();
	tiles[p_atlas_coords].alternatives_ids.push_back(new_alternative_id);
	tiles[p_atlas_coords].alternatives_ids.sort();
	_compute_next_alternative_id(p_atlas_coords);
	emit_signal(SNAME("changed"));
	return new_alternative_id;
}
void TileSetAtlasSource::remove_alternative_tile(const Vector2i p_atlas_coords, int p_alternative_tile) {