You are right. Apple is fully in control of the servers and the software, and there is no way for a customer to verify Apple's claims. Nevertheless system transparency is a useful concept. It can effectively reduce the number of things you have to blindly trust to a short and explicit list. Conversely it forces the operator, in this case Apple, to explicitly lie. As others have pointed out, that is quite a business risk.
As for transparency logs, it is an amazing technology which I can highly recommend you take a look at in case you don't know what it is or how it works. Check out transparency.dev or the project I'm involved in, sigsum.org.
> they are almost guaranteed to be misusing that data
That is very unlikely because of the liability, as others have pointed out. They are making claims which the Apple PCC architecture helps make falsifiable.