If you want to put (most of) your config files in a .config folder, then most apps should support that
If you want to view your config files in a different way, then actually you're trying to solve a different problem. Perhaps hide show toggling or automatic grouping (see macOS desktop stacks) with your fs viewer would be a better area to tackle.
Finally, just wanted to say, everything at root level is usually config or a folder, so if I want to understand what tooling a project uses, I know immediately where to go, code is always in a "src" or similar. It sounds like this is a feature, not a bug.