### 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)
set_navigation_polygon(layer_index, polygon);
			return true;
		}
	} else if (components.size() == 2 && components[0] == "terrains_peering_bit") {
		
		for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
			if (components[1] == TileSet::CELL_NEIGHBOR_ENUM_TO_TEXT[i]) {
				set_terrain_peering_bit(bit, p_value);
				return true;
			}
		}
		return false;
	} else if (components.size() == 1 && components[0].begins_with("custom_data_") && components[0].trim_prefix("custom_data_").is_valid_int()) {
		
		int layer_index = components[0].trim_prefix("custom_data_").to_int();
		ERR_FAIL_COND_V(layer_index < 0, false);
		if (layer_index >= custom_data.size()) {
			if (tile_set) {
				return false;
			} else {
				custom_data.resize(layer_index + 1);
			}
		}
		set_custom_data_by_layer_id(layer_index, p_value);
		return true;
	}
	return false;
}
bool TileData::_get(const StringName &p_name, Variant &r_ret) const {