Grr. You can always tell when somebody has been on the NAS or done any development work on a branch checked out of source control on a MacBook...
The development work thing isn't the fault of Apple, but rather the stupid developer who didn't pay attention to their commit.
I think there's plenty of blame to go to both of them. There's no defensible reason to put dotfiles in every single folder, and there are many, many reasons why it may not be desired of various levels of vehemence.
Oh look, OSX has touched this usb stick, and vomited it's dotfiles onto it. Did it ever write to the stick? Nope, just need to throw those trash dotfiles onto every. single. thing. it. sees.