you're saying that CCleaner is a bad idea simply because they cannot possibly understand the registry well enough to make the changes that they're making.
It sounds more like, "the software vendor is doing incorrect or incomplete things with the registry and CCleaner cannot possibly know that."
As a long-time Windows software developer, I've been stunned at how sloppy desktop programs and installers are, even today. People ignore Microsoft guidelines, somehow get the software to the "works for me" stage, and deploy it.