### 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(p_peering_bit == TileSet::CELL_NEIGHBOR_MAX, -1);
	ERR_FAIL_COND_V(!is_valid_bit[p_peering_bit], -1);
	return bits[p_peering_bit];
}
void TileSet::TerrainsPattern::from_array(Array p_terrains) {
	set_terrain(p_terrains[0]);
	int in_array_index = 1;
	for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
		if (is_valid_bit[i]) {
			ERR_FAIL_INDEX(in_array_index, p_terrains.size());
			set_terrain_peering_bit(TileSet::CellNeighbor(i), p_terrains[in_array_index]);
			in_array_index++;
		}
	}
}
Array TileSet::TerrainsPattern::as_array() const {
	Array output;
	output.push_back(get_terrain());
	for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
		if (is_valid_bit[i]) {
			output.push_back(bits[i]);
		}
	}
	return output;
}
TileSet::TerrainsPattern::TerrainsPattern(const TileSet *p_tile_set, int p_terrain_set) {