As Dave rightly says, Qantas does offer the option to book and pay for different classes. They are one of the few FF programs that offers one-way redemptions, which was one of the promoted benefits of the last round of major enhancements. So the member is able to book the different components in different classes if desired. But if booking separate redemptions, the fuel fines are charged per segment and not at the discounted rate for a through flight to Europe.
Now how about this hypothetical situation:
FF member books a round trip redemption at the F rate, with a mixture of F where available and J when only 2-class flights are available. As an example, say 3 of the flights are in F and 4 of the flights are in J. All booked and tickets issued. Member is happy to pay the F rate as 70% of the journey will be in F and 30% in J.
Then a few months later, say one of the operating airlines (a partner airline not the member's FF program operator) decides to remove F from one of the routes, resulting in a re-issue of the ticket into J for that sector. Now the journey will be less than 40% in F and more than 60% in J.
Now its too late to rebook the entire journey in J as there is no availability for J awards on the remaining F segments and no possible re-route with award seats available for a month either side of the travel dates. F award has cost 100K more points than a J award for the same route.
An unfortunately situation and a risk when booking FF redemptions 11 months out. But nought can be done except to accept the lack of F on the segment and look forward to travelling in J.
The difference with the example I mention is that the member made the booking for F and paid for F and had the ticket issued for F and now has to travel in J. The OP of this thread made the booking for some segments in Y and had the ticket issued for that cabin. Availability of J seats is not relevant. If there is availability if U seats then they can cancel and rebook, remembering that U does not permit waitlisting.
What about a passenger who has purchased a OneWorld Explorer such as DONE4. The rules say that if no D is available, then it books into L. It is quite possible that a flight may have J for sale but no D and the passenger remains in the economy cabin. In this case the pax has paid for a business class fare and its quite possible there will be empty business class seats. But no D for sale. Its even possible the pax could waitlist for a FF points upgrade which may clear even though there is no D available.