Is working on finishing already existing, illegally built apartments, after their construction has been completed, considered unlawful, despite their status being regularized with the state later on?

There is no harm in finishing apartments built in violation of building codes, because the state reconciles these violations, which means there is no apparent harm, and because the state may amend the law later and permit these additions. Obedience to the ruler in restricting permissible matters is obligatory if there is a clear benefit, otherwise not.