Looks like the option to publish after transcoding does something sane in the new PeerTube beta. It does the initial transcode, mid-range resolution version, and then publishes before doing additional higher and lower resolution versions (so transcode ordering is also different). Glad to use that feature from now on instead of having to monitor what's going on (not a good option for non-admins, this would be extra frustrating if I were just a user) to avoid publishing something broken.