### 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)
TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {
				Vector2i neighbor = tile_map_node->get_neighbor_cell(coords, bit);
				if (!can_modify_set.has(neighbor)) {
					can_modify_list.push_back(neighbor);
					can_modify_set.insert(neighbor);
				}
			}
		}
	}
	
	RBSet<TerrainConstraint> constraints;
	
	for (Vector2i coords : p_coords_array) {
		
		RBSet<TerrainConstraint> added_constraints = _get_terrain_constraints_from_added_pattern(coords, p_terrain_set, p_terrains_pattern);
		for (TerrainConstraint c : added_constraints) {
			c.set_priority(10);
			constraints.insert(c);
		}
	}
	
	for (TerrainConstraint c : _get_terrain_constraints_from_painted_cells_list(painted_set, p_terrain_set, p_ignore_empty_terrains)) {
		constraints.insert(c);
	}
	
	output = terrain_fill_constraints(can_modify_list, p_terrain_set, constraints);
	return output;
}
TileMapCell TileMapLayer::get_cell(const Vector2i &p_coords, bool p_use_proxies) const {