**Update**
I again contacted the airline today to ask about this flight scenario.
I explained that I am looking at a multi-city booking, with flight 1 MEL-LAX, then flight 2 being LAX-JFK the next morning and asked if this would have any conflict with the airline's cabotage policy in the US.

They started off by saying that any flight results that come up on the Qantas website's booking engine are all legitimate/confirmed.

I then repeated that it was a multi-city booking, to which the staff conveyed that all multi-city legs are considered one-way flights.
I asked if this would then consider flight #2 LAX-JFK ineligible given it would then be considered a 'domestic' leg - and the staff agreed with me.
But went onto say that I should double check with the airline staff at the airport as they may be able to make it work(?).


I have since had another look using the Qantas website's booking engine and instead of making a multi-city:MEL-LAX, LAX-JFK booking, I instead looked at MEL-JFK as a direct route and on the same date.
The results showed that Thursday night's QF95 MEL-LAX, does not form a combination with Friday mornings QF11 LAX-JFK flight as an option that comes up in the booking search.


From that I take it my preferred multi-city booking option of checking in at LAX the following morning to join QF11 will be ineligible as it would be a separate flight from my transpac flight from Australia to America 13 hours earlier the previous day.
(Qantas wouldn't even have a check in desk open at LAX in the morning for QF11 would they, rather just a transfers counter for those passengers who arrived the same morining from Australia on QF93/QF11/QF15 right?)

For my LAX-JFK flight I pretty keen for a window seat, so I don't think I'll take the risk and book QF11, just incase I get moved to a different flight instead where I assume it will be highly unlikely that I would get select my seat as a 'standby' passenger.
I'll instead now book this flight separately with another carrier.

In conclusion I am still a little confused and disappointed as to why QF11 LAX-JFK is still coming up as a flight option on the multicity booking engine results.