### 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)
break;
							default:
								break;
						}
						if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
							polygon = _get_half_offset_corner_or_side_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, bit);
						} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
							polygon = _get_half_offset_corner_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, bit);
						} else { 
							polygon = _get_half_offset_side_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, bit);
						}
					}
					{
						Ref<ArrayMesh> mesh;
						mesh.instantiate();
						Vector<Vector2> uvs;
						uvs.resize(polygon.size());
						Vector<Color> colors;
						colors.resize(polygon.size());
						colors.fill(Color(1.0, 1.0, 1.0, 1.0));
						Array a;
						a.resize(Mesh::ARRAY_MAX);
						a[Mesh::ARRAY_VERTEX] = polygon;
						a[Mesh::ARRAY_TEX_UV] = uvs;
						a[Mesh::ARRAY_COLOR] = colors;
						a[Mesh::ARRAY_INDEX] = Geometry2D::triangulate_polygon(polygon);
						mesh->add_surface_from_arrays(Mesh::PRIMITIVE_TRIANGLES, a, Array(), Dictionary(), Mesh::ARRAY_FLAG_USE_2D_VERTICES);
						terrain_peering_bits_meshes[terrain_mode][bit] = mesh;
					}
				}