### 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)
}
	p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Custom Data", ""), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_GROUP));
	for (int i = 0; i < custom_data_layers.size(); i++) {
		p_list->push_back(PropertyInfo(Variant::STRING, vformat("custom_data_layer_%d/name", i)));
		p_list->push_back(PropertyInfo(Variant::INT, vformat("custom_data_layer_%d/type", i), PROPERTY_HINT_ENUM, argt));
	}
	
	
	for (const KeyValue<int, Ref<TileSetSource>> &E_source : sources) {
		p_list->push_back(PropertyInfo(Variant::INT, vformat("sources/%d", E_source.key), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR));
	}
	
	
	p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Tile Proxies", ""), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_GROUP));
	p_list->push_back(PropertyInfo(Variant::ARRAY, PNAME("tile_proxies/source_level"), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR));
	p_list->push_back(PropertyInfo(Variant::ARRAY, PNAME("tile_proxies/coords_level"), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR));
	p_list->push_back(PropertyInfo(Variant::ARRAY, PNAME("tile_proxies/alternative_level"), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR));
	
	for (unsigned int pattern_index = 0; pattern_index < patterns.size(); pattern_index++) {
		p_list->push_back(PropertyInfo(Variant::OBJECT, vformat("pattern_%d", pattern_index), PROPERTY_HINT_RESOURCE_TYPE, "TileMapPattern", PROPERTY_USAGE_NO_EDITOR));
	}
}
void TileSet::_validate_property(PropertyInfo &p_property) const {
	if (p_property.name == "tile_layout" && tile_shape == TILE_SHAPE_SQUARE) {
		p_property.usage ^= PROPERTY_USAGE_READ_ONLY;
	} else if (p_property.name == "tile_offset_axis" && tile_shape == TILE_SHAPE_SQUARE) {
		p_property.usage ^= PROPERTY_USAGE_READ_ONLY;
	}
}
void TileSet::_bind_methods() {