"...since the normal filesystem inside the container is ephemeral."

Not by default:

  # docker run -i -t ubuntu bash
  root@48dbef418f4c:/# echo foo > /bar
  root@48dbef418f4c:/# exit
  # docker restart 48dbef418f4c
  48dbef418f4c
  # docker attach 48dbef418f4c
  root@48dbef418f4c:/# cat /bar
  foo
  root@48dbef418f4c:/#

Docker won't delete a container unless you tell it to.