Could it be an issue with your Joplin-Server Container? I've done my Upgrade with the original Joplin-Server Container and it works.
Maybe you find a way with this Post. I was just copying Code snippets and don't know realy what I do. 
But it works.
Edit:
It looks like I've used another command to restore the Database:
docker exec joplin_db pg_restore --clean -U joplin -d joplin /var/lib/postgresql/data/backup.dump
"joplin" hast to be changed by you.
-U joplinServer -d joplinServerDb
Oh. And I have used a custom Format for the Backup. "-Fc" *.dump. I don't know If this is important.
Edit 2:
And I've made no dumpall. 
I only saved the Database.