There's a proposal at the linked blog post for how to clean up the config directory.

The post goes into detail which changes would be required in KDE software using Qt.

After reading, I just have one question (the blog does not seem to have a comment section): how does this handle transitioning from the old location to the new location? Imagine having a katerc config file under ~/.config and one under ~/.config/kate (which is the suggestion from the post) - should those be merged once and then the old one gets deleted?