The real issue is who gets to sign the code. Formerly, you could sign the code yourself, so the cryptographic "chain of custody" between you and your users would be preserved. Now, since Apple generates the code that users see, you can't check and sign it. Apple can sign it, somebody who has compromised Apple's infrastructure can sign it, but you can't (unless you're the one who compromised their infrastructure). So, basically, this is a giant MITM just waiting to be exploited.