### 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)
TileData *tile_data = atlas_source->get_tile_data(cell.get_atlas_coords(), cell.alternative_tile);
				if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
					current_pattern = tile_data->get_terrains_pattern();
				}
			}
		}
		TileSet::TerrainsPattern pattern = _get_best_terrain_pattern_for_constraints(p_terrain_set, coords, constraints, current_pattern);
		
		RBSet<TerrainConstraint> new_constraints = _get_terrain_constraints_from_added_pattern(coords, p_terrain_set, pattern);
		for (const TerrainConstraint &E_constraint : new_constraints) {
			if (constraints.has(E_constraint)) {
				constraints.erase(E_constraint);
			}
			TerrainConstraint c = E_constraint;
			c.set_priority(5);
			constraints.insert(c);
		}
		output[coords] = pattern;
	}
	return output;
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMapLayer::terrain_fill_connect(const Vector<Vector2i> &p_coords_array, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	HashMap<Vector2i, TileSet::TerrainsPattern> output;
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND_V(!tile_set.is_valid(), output);
	ERR_FAIL_INDEX_V(p_terrain_set, tile_set->get_terrain_sets_count(), output);
	
	Vector<Vector2i> can_modify_list;
	RBSet<Vector2i> can_modify_set;