The driver wraps all queries in the $query meta operator. However, the $cmd collection doesn't seem to respect that and closes the connection causing an EndOfStreamException in the driver.

The does NOT affect general purpose commands. Rather, it affects something like this, getting the current op:

var result = client
                .GetDatabase("admin")
                .GetCollection<BsonDocument>("$cmd.sys.inprog")
                .Find(new BsonDocument("$all", true))
                .ToListAsync()
                .GetAwaiter().GetResult();