### 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)
Transform2D xform;
							xform = flip_h ? xform.scaled(Size2(-1, 1)) : xform;
							xform = flip_v ? xform.scaled(Size2(1, -1)) : xform;
							xform = transpose ? Transform2D(xform[1], xform[0], Vector2()) : xform;
							int alternative_tile = 0;
							if (!atlas_source->has_tile(coords)) {
								atlas_source->create_tile(coords);
							} else {
								alternative_tile = atlas_source->create_alternative_tile(coords);
							}
							
							Array key_array;
							key_array.push_back(coords);
							key_array.push_back(flip_h);
							key_array.push_back(flip_v);
							key_array.push_back(transpose);
							Array value_array;
							value_array.push_back(source_id);
							value_array.push_back(coords);
							value_array.push_back(alternative_tile);
							if (!compatibility_tilemap_mapping.has(E.key)) {
								compatibility_tilemap_mapping[E.key] = RBMap<Array, Array>();
							}
							compatibility_tilemap_mapping[E.key][key_array] = value_array;
							compatibility_tilemap_mapping_tile_modes[E.key] = COMPATIBILITY_TILE_MODE_ATLAS_TILE;
							TileData *tile_data = atlas_source->get_tile_data(coords, alternative_tile);
							tile_data->set_flip_h(flip_h);
							tile_data->set_flip_v(flip_v);
							tile_data->set_transpose(transpose);
							tile_data->set_material(ctd->material);