I would like to suggest that spreading CSS in multiple files and keeping it deliberately ordered are not mutually exclusive choices, at least in my experience. As long as you never rely on the file system for ordering — i.e. you manually decide the order in which files are imported — then you can have the best of both worlds.
In principle, the well-commented file does not disappear; it is still there, orchestrating the cascade.
I would go as far as saying that messing up with specificity is orthogonal to whether you decide to split your CSS in multiple files or not: even in a single file, it’s easy to get it wrong.