If you mean migrating the files yourself, it’s just a matter of copying the file from the old place ~/.config/yourconfigrc to ~/.config/yourapp/yourconfigrc.
If you mean you want the application to manage the migration itself, that’s an implementation detail I hadn’t thought about yet, but which I assume wouldn’t be difficult to do with KConfig.
Just for clarification: this would be a one-time process per application, right? I’m sure this will work for 99% of users, but there’ll always be the one (or a couple of users) that synchronizes their .config directory, then doesn’t update all machines at the same time and all hell breaks loose - a.k.a xkcd.com/1172/ :-) But I’d say that’s probably not worth losing the advantages of a cleaner .config-directory, so this might be one of those “tough-luck” situations… 🤷