### 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(!is_valid_terrain_peering_bit(p_peering_bit), -1);
	return terrain_peering_bits[p_peering_bit];
}
bool TileData::is_valid_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit) const {
	ERR_FAIL_NULL_V(tile_set, false);
	return tile_set->is_valid_terrain_peering_bit(terrain_set, p_peering_bit);
}
TileSet::TerrainsPattern TileData::get_terrains_pattern() const {
	ERR_FAIL_NULL_V(tile_set, TileSet::TerrainsPattern());
	TileSet::TerrainsPattern output(tile_set, terrain_set);
	output.set_terrain(terrain);
	for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
		if (tile_set->is_valid_terrain_peering_bit(terrain_set, TileSet::CellNeighbor(i))) {
			output.set_terrain_peering_bit(TileSet::CellNeighbor(i), get_terrain_peering_bit(TileSet::CellNeighbor(i)));
		}
	}
	return output;
}
void TileData::set_navigation_polygon(int p_layer_id, Ref<NavigationPolygon> p_navigation_polygon) {
	ERR_FAIL_INDEX(p_layer_id, navigation.size());
	navigation.write[p_layer_id] = p_navigation_polygon;
	emit_signal(SNAME("changed"));
}
Ref<NavigationPolygon> TileData::get_navigation_polygon(int p_layer_id) const {
	ERR_FAIL_INDEX_V(p_layer_id, navigation.size(), Ref<NavigationPolygon>());
	return navigation[p_layer_id];
}
void TileData::set_probability(float p_probability) {