Like I say, that particular piece of Google play developer terms of service is nothing new, it's been in place for years. It's there to protect users from apps downloading malicious content files after being installed from the play store.
You probably know me well enough at this point to know that if there was even the slightest whiff that Google were doing anything wrong I would be shouting about it louder than anyone else lol. But I honestly think that article is basically just FUD for clicks.
I don't remember ever using total commander , so i don't know if they were actually doing anything wrong or if this is just google miss classify in the app . But i am almost certain that it is one of those two things .