No, the routing is as listed (with QF 107 SYD-JFK as one segment).

I spoke with the TA today, who said "too many connections". I started off trying to explain "transit without stopover" vs. "stopovers" for the PER-MEL-BNE, but ended up getting that feeling that she wasn't following me. I thought of using the example "but imagine I lived in Mt Isa and had to travel ISA-BNE-SYD to start and finish my journey.."
Ended up just saying to check it directly with QF, and if they haven't figured it out by Monday, I will call QF myself to sort it.

It must be a sign of frequenting FT too much when you find yourself trying to explain subtle details of OneWorld products to people in the travel industry!

Thanks to all for the advice too.
I'll let you know what it takes to get it sorted (and then I can put an entry in the QF upgrade lottery for the QF 107 and QF10 segments!)