Original question: Where is confidential data held and how is access to it controlled? response: It depends on the context, but if you include metadata in a transaction, those metadata will be publicly available. However, you can always encrypt your metadata. When you encrypt metadata and attach it to a UTXO, whoever else has the secret key to decrypt those metadata will be able to read decipher it, but nobody else will be able to.
Additional questions related to above: For holding confidential data: I see how encrypting data on chain can keep it confidential for some years until the crypto is broken and maybe that’s OK for some data and expectations of confidentiality. Quorum (when last I spoke to them) don’t put encrypted data on chain since they share my assumption that crypto works for a limited time. How would access to the secret key you mention be tied to UTXO? I don’t see that linkage