I would question your assumption that "clean code" that you describe is really modularization and abstraction. (In particular, separating everything into small scattered pieces, which is IMHO a horrible Java habit that I have to endure now.)
I mean, both modules and abstractions should have purpose.
The purpose of modules is to "do one task well" so to speak. So if for a typical change you need to modify several of them, you're not modularizing it right.
The purpose of abstraction is to provide another "language" which lets you forget certain technical details, while clarifying the bigger picture. Again, unless this language has been designed wrong, you shouldn't have to touch the abstraction.
I mean, both modules and abstractions should have purpose.
The purpose of modules is to "do one task well" so to speak. So if for a typical change you need to modify several of them, you're not modularizing it right.
The purpose of abstraction is to provide another "language" which lets you forget certain technical details, while clarifying the bigger picture. Again, unless this language has been designed wrong, you shouldn't have to touch the abstraction.
Addendum: Of course, there is also the classic https://gbracha.blogspot.com/2011/06/types-are-anti-modular.... (and we can consider types to be a form of abstraction), so to some extend these things go against one another.