### 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_INDEX_V(p_layer_id, custom_data_layers.size(), "");
	return custom_data_layers[p_layer_id].name;
}
void TileSet::set_custom_data_layer_type(int p_layer_id, Variant::Type p_value) {
	ERR_FAIL_INDEX(p_layer_id, custom_data_layers.size());
	custom_data_layers.write[p_layer_id].type = p_value;
	for (KeyValue<int, Ref<TileSetSource>> &E_source : sources) {
		E_source.value->notify_tile_data_properties_should_change();
	}
	emit_changed();
}
Variant::Type TileSet::get_custom_data_layer_type(int p_layer_id) const {
	ERR_FAIL_INDEX_V(p_layer_id, custom_data_layers.size(), Variant::NIL);
	return custom_data_layers[p_layer_id].type;
}
void TileSet::set_source_level_tile_proxy(int p_source_from, int p_source_to) {
	ERR_FAIL_COND(p_source_from == TileSet::INVALID_SOURCE || p_source_to == TileSet::INVALID_SOURCE);
	source_level_proxies[p_source_from] = p_source_to;
	emit_changed();
}
int TileSet::get_source_level_tile_proxy(int p_source_from) {
	ERR_FAIL_COND_V(!source_level_proxies.has(p_source_from), TileSet::INVALID_SOURCE);
	return source_level_proxies[p_source_from];
}
bool TileSet::has_source_level_tile_proxy(int p_source_from) {
	return source_level_proxies.has(p_source_from);
}
void TileSet::remove_source_level_tile_proxy(int p_source_from) {