### 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)
ERR_FAIL_COND_V(p_value.get_type() != Variant::STRING, false);
				while (index >= custom_data_layers.size()) {
					add_custom_data_layer();
				}
				set_custom_data_layer_name(index, p_value);
				return true;
			} else if (components[1] == "type") {
				ERR_FAIL_COND_V(p_value.get_type() != Variant::INT, false);
				while (index >= custom_data_layers.size()) {
					add_custom_data_layer();
				}
				set_custom_data_layer_type(index, Variant::Type(int(p_value)));
				return true;
			}
		} else if (components.size() == 2 && components[0] == "sources" && components[1].is_valid_int()) {
			
			int source_id = components[1].to_int();
			if (has_source(source_id)) {
				remove_source(source_id);
			}
			add_source(p_value, source_id);
			return true;
		} else if (components.size() == 2 && components[0] == "tile_proxies") {
			ERR_FAIL_COND_V(p_value.get_type() != Variant::ARRAY, false);
			Array a = p_value;
			ERR_FAIL_COND_V(a.size() % 2 != 0, false);
			if (components[1] == "source_level") {
				for (int i = 0; i < a.size(); i += 2) {
					set_source_level_tile_proxy(a[i], a[i + 1]);
				}