I've also never found my-self working with a code-base I'd considered clean and highly maintainable. When code-bases becomes big and complex, they tend to get messy. It's hard, if not impossible, to maintain a complete view of the entire application at once - and this leads to different approaches at different times, and places in the code. Having multiple developers come and go, with various levels of skills, does not help either. Having some framework dictate the overall structure of the application limits the potential for to much diversity in the code, it also helps new developers get a grasp of the codebase if they have used the framework, or similar frameworks, in the past.
When I design a simple application, the flow is limited, and I don't need the abstractions - so I don't implement them. But when the system grows in complexity, and the concepts and logic starts to overlap, it becomes reasonable to implement abstractions. To layer the application into DAO, service, persistence layer, etc. To group common logic, and make abstract implementations. I could go on. Abstractions are good, but overuse is also not good - of-course, like everything else it's about finding the right balance.