See now, that's quite unrelated what I'm envisioning, or the topic of the OP's article, but that's definitely the way we're headed in terms of file handling.
"File-type strictly associated with app" is good for security and it's good for people's mental organization. Unfortunately you're referring strictly to local file storage, I assume, and practically nothing on my phone is in local storage but "in the cloud". The only local storage I use is for ringtones and certain audiobooks/prayers which I enjoy listening whether or not I'm connected to a network.
It would seem that data centers and cloud services are a long way from "file types strictly associated with app" and also the sort of behavior you describe would be really horrible and undesirable in a typical data-center setting. I mean, I can't even imagine how it'd be implemented, given that data storage is often remote or at least decoupled from the "application server", and it's definitely never a 1:1 relationship between those abstracted components.
Can you imagine needing to "delete the /bin/tar application" in order to purge every file ending in ".tar" or ".tgz"?
But it's true that the new mobile OS paradigm has advantages for cleanup. If you've got a 3rd-party app and you've created some big crap files with it, and you uninstall that app, then it's a clean sweep when it takes along all the crap and you don't need to worry about lingering loose ends, or files you simply can't open, because their handler's gone.
Scoped storage is way more secure; it's also wonderful on my Androids that I can selectively grant access to files and media, rather than giving "the keys to the kingdom" to all these Social Media apps. I definitely never want to post my bank screenshots to Facebook and the possibility no longer looms!
These days I am sort of nonplussed when a web app demands an all-access pass to my Google Drive, because permissions can be appropriately scoped now, and the app can play in its own Drive "Sandbox" without having access to my spreadsheets and medical records. I just wish that there were some really good "cleanup" apps. Remember those "cleanup" programs that would come with antivirus for your PC, or Regclean, or whatever freeware utility would purport to liberate your 10MB HDD? Those were good times.
It's the same with social media posts--I often wish to really scrub my account, delete all posts and all comments and basically all activity, and while that's possible on Facebook it's arduous and it takes me weeks to scrub the major stuff after 4-5 years. But I only think of it on Shrovetide Monday or Fat Tuesday, and then I spend 3 weeks in Lent doing scrub, scrub, scrub. Sometimes the mouse/keyboard gestures are more repetetive & physically demanding than cleaning the toilet. Way too difficult, and that's by design.