### 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)
break;
				case 3:
					output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_CORNER;
					output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_LEFT_CORNER;
					output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_LEFT_CORNER;
					break;
				case 4:
					output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_SIDE;
					output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_SIDE;
					break;
				case 5:
					output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE;
					output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE;
					break;
				default:
					ERR_FAIL_V(output);
			}
		}
	}
	return output;
}
TerrainConstraint::TerrainConstraint(const TileMap *p_tile_map, const Vector2i &p_position, int p_terrain) {
	tile_map = p_tile_map;
	Ref<TileSet> ts = tile_map->get_tileset();
	ERR_FAIL_COND(!ts.is_valid());
	bit = 0;
	base_cell_coords = p_position;
	terrain = p_terrain;
}
TerrainConstraint::TerrainConstraint(const TileMap *p_tile_map, const Vector2i &p_position, const TileSet::CellNeighbor &p_bit, int p_terrain) {