Every single program has to write logic to parse/store/query/validate those values. A common API with a single store can be type-enforced, backed up, and likely easier to work with from an internationalization perspective.

I do like dotfiles for portable apps where everything the program needs is in one folder. Personally, my need for portable apps has gone down year on year.

I'm the opposite: I'll take a centralized, strongly-typed registry over 'stringly' typed dotfiles scattered across the entire filesystem.