eg. ~./bashrc has existed there for 30+ years, changing stuff just because someone doesn't like seeing a file in a folder is imho stupid.
But when people are talking about compliance, and hardcoding very few people are talking about those applications - there are hundreds of other applications do the wrong thing, and some scripts hardcode things as a result.
If you get to the point where you need another file for something, put it in a directory under .config so whenever you need to add even more, you don't keep cluttering my home.
This also had the side effect of hiding entries that had names beginning with ".", and over time an implementation bug/quirk became accepted behaviour, and was post-hoc rationalised as "hidden" files.