The key in the desktop version is not always stored in the secure enclave, is my assumption (it definitely supports plaintext storage). Theoretically this makes it possible to extract the key for the message database. Also a different malicious program can read it. But this is moot anyway if the FBI can browse through the chats. This isn't what failed here.

Also last time I looked (less than 1 year ago) files sent over Signal are stored in plain, just with obfuscated filenames. So even without access to Signal it's easy to see what message attachments a person has received, and copy any interesting ones.