The segments are origin/destination regardless of whether they are direct or non-stop. In other words, there is a distinct difference between JFK-LAX-SYD and JFK-SYD via LAX. The first counts as two segments and one would be considered your transcon. The other is one segment and it is not considered your transcon irrespective of whether it goes through Los Angeles.

The short answer to your concern is that JFK-SYD is not considered a transcon flight. Do keep in mind, however, that it does not run every day whereas the LAX flight does.