The other kink is that the secret server itself reads the secrets from a symmetrically-encrypted file and when it boots, it doesn't actually know how to decrypt it. There's a master key for this that's stored GPG encrypted so that a small number of people can retrieve it and use a client tool that sends the secret server an "unlock" command containing the master key. So any time a secret server reboots, someone with access needs to gpg --decrypt mastersecret | secret_server_unlock_command someserver
There are some obvious drawbacks to this whole system (constraining pushes to require an SSH agent connection is a biggie and wouldn't fly some places, and agent forwarding is not without its security implications) and some obvious problems it doesn't solve (secrets are obviously still in RAM), but on the whole it works very well for distributing secrets to a large number of apps, and we have written tools that have basically completely eliminated any individual's need to ever actually lay eyes on a secret (e.g. if you want to run any tool in the mysql family, there's a tool that fetches the secret for you and spawns the tool you want with MYSQL_PWD temporarily set in the env, so you need not copy/paste it or be tempted to stick it in a .my.cnf).