Is it permissible for an engineer to sell leftover items from his work on a villa, knowing that the villa owner has paid their price to the company, and he (the owner) does not benefit from them?

What the villa owner leaves behind out of disinterest, you are permitted to benefit from it for yourself, whether by selling it or other means, and you are not obligated to give it to the company. For whoever comes first to something permissible, or what people cast aside out of disinterest, has a greater right to it.