### 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)
Vector2i neighbor = tile_map_node->get_neighbor_cell(coords, bit);
					if (cells_with_terrain_center_bit.has(neighbor)) {
						constraints.insert(c);
					}
				} else {
					
					HashMap<Vector2i, TileSet::CellNeighbor> overlapping_terrain_bits = c.get_overlapping_coords_and_peering_bits();
					bool valid = true;
					for (KeyValue<Vector2i, TileSet::CellNeighbor> kv : overlapping_terrain_bits) {
						if (!cells_with_terrain_center_bit.has(kv.key)) {
							valid = false;
							break;
						}
					}
					if (valid) {
						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;
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMapLayer::terrain_fill_path(const Vector<Vector2i> &p_coords_array, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {