I also do third party software development, and my approach is always: bill (highly, $300+/hr) for the features and requirements, but do the manual refactoring and architecture/performance/detail work on your own time. It benefits you, it benefits the client, it benefits the relationship, and it handles the misunderstanding of your normie clients with regard to what constitutes "working".

Say it takes 2 hours to implement a feature, and another hour making it logically/architecturally correct. You bill $600 and eat $200 for goodwill and your own personal/organizational development. You're still making $200/hr and you never find yourself in meetings with normie clients about why refactoring, cohesiveness, or quality was necessary.