Imagine connecting to a Jitsi or Etherpad service over HTTPS - all you get is some assurance that the remote system is operated by the owner of a specific DNS name. Now imagine the same situation, but you also have a browser extension that verifies that the boot chain of the remote system is reproducible and discoverable in a transparency log.
As I mentioned elsewhere in this thread, System Transparency aims to make the reachable state space of a remote system discoverable. Imagine your web browser being able to verify whether you're connecting to a Jitsi server, or a Jitsi server which also records all meetings.
You're absolutely right that there are lots of limitations and things that can't be mathematically proven, but that goes for any defensive security technology.
For sure remote attestation can be used against the interests of the user, but it can also very much be used for the interests of the user. Imagine a world where you don't have to trust online services blindly.