### 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 TileSet::CELL_NEIGHBOR_TOP_RIGHT_CORNER:
					bit = 3;
					base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_SIDE);
					break;
				case TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE:
					bit = 5;
					base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE);
					break;
				default:
					ERR_FAIL();
					break;
			}
		}
	}
	terrain = p_terrain;
}
#define TILEMAP_CALL_FOR_LAYER(layer, function, ...) \
	if (layer < 0) {                                 \
		layer = layers.size() + layer;               \
	};                                               \
	ERR_FAIL_INDEX(layer, (int)layers.size());       \
	layers[layer]->function(__VA_ARGS__);
#define TILEMAP_CALL_FOR_LAYER_V(layer, err_value, function, ...) \
	if (layer < 0) {                                              \
		layer = layers.size() + layer;                            \
	};                                                            \
	ERR_FAIL_INDEX_V(layer, (int)layers.size(), err_value);       \
	return layers[layer]->function(__VA_ARGS__);
Vector2i TileMap::transform_coords_layout(const Vector2i &p_coords, TileSet::TileOffsetAxis p_offset_axis, TileSet::TileLayout p_from_layout, TileSet::TileLayout p_to_layout) {