Unless I'm missing something, the only time the issue of which NA segment is the extra purchased one would come into play on an initial purchase would be if the passenger wanted to purchase it in a lower class of service than the *ONE*.

As to why they want purchased segments to be after the free ones, I can see a rationale involving complications during ticket reissue. What if you had the extra purchased segment as the first segment in NA, flew it, then later changed the ticket such that you no longer had extra segments? This would complicate the reprice and possible refund.