I've looked at this further and when doing a test booking on the JAL site the seat map preview in the flight selection screen shows the full range of seats but when it gets to the booking process the same restricted range applies. On a multi city you can't chose the fare level. When booking a straight return you can choose the fare level which has 3 options with the middle being economy semi flex but even that has the same seat selection again. So no way to get a suitable fare level for the better seats on the outbound flight unless presumably choosing the full economy fare which costs more than business.

Just to annoy me a bit more the price has dropped since I booked as well, i'd almost come out on top if I cancel and rebook (allowing for cancel fee).