SYD-MEL is a 1 hour day-time flight, so Skybed is not really a benefot on that sector. The NRT-SYD, NRT-MEL or ICN-SYD are going to be overnight so they are the ones you want best comfort.

Transit in SYD means access to the Qantas Club lounges, so chance for shower, food, booze at international terminal. Transit in NRT means access to the QF lounge operated by JAL. That lounge has free wirless internet (ask reception for access) btu no showers and limited food.

Looks like its not going to make a great deal of difference. I would go for the best schedule timing or most SC's to be earned.