The fedora remote is now delivered via the fedora-ostree-repos package, which allows the Fedora/Silverblue teams to deliver configuration changes via the RPM (and subsequent Silverblue composes).
Previously, the fedora-workstation remote was not delivered via an RPM and was configured as part of the post-compose process. This made it difficult to deploy changes to all Silverblue users.
The main difference between the two is the configuration. The fedora remote points at a new set of infrastructure that improves the download speeds of ostree content.
$ cat /etc/ostree/remotes.d/fedora.conf
[remote "fedora"]
url=https://ostree.fedoraproject.org
gpg-verify=true
gpgkeypath=/etc/pki/rpm-gpg/
contenturl=mirrorlist=https://ostree.fedoraproject.org/mirrorlist
The fedora-workstation remote references the legacy infrastructure that was previously used. This config is still usable (for now), but it will likely result in slower download speeds.
$ cat /etc/ostree/remotes.d/fedora-workstation.conf
[remote "fedora-workstation"]
url=https://kojipkgs.fedoraproject.org/atomic/repo/
gpg-verify=true
gpgkeypath=/etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-29-primary