You have to trust the instance admin you are joining; the same goes for Lemmy/Mastodon/XMPP. The instance owner can see your IP address, your devices, email etc. They can act on your behalf - so basically they have a fair amount of control over your account. But they cannot see any encrypted content. These issues are a bit hard to solve in case of something like Matrix often at performance costs; same goes for the metadata issue.

If you want to self host you can run a de-federated instance for only personal use or you can run it as a onion hidden service - this way the metadata issue is solved. But note that Synapse is pretty resource intensive.