The problem is that all food has to be declared, although much of it (including chocolate) will then be allowed in. By your argument, airlines flying to NZ shouldn't serve any food, as anything from the meal or snack needs to be declared, and Customs could decide not to allow it. Expecting QF to only serve "legally importable" food means they have to know exactly what Customs may or may not allow. Sure, QF know you can't take in an apple, but can you bring the cheese from your meal, or the muesli bar? Rather than QF restricting their menu to NZ-allowable items, they do inform you (over and over) that you have to declare all food and let Customs make the call.

I had a young colleague get caught out at Australian Customs when they x-rayed his bag and found a tin of teabags. While they're allowable, he hadn't declared it and got a long stern lecture. They would have been justified in fining him but they could see it was an honest misunderstanding (he still can't see how "teabag" = "food") and they let him off. It's nice to get mercy but if you get justice instead, you can't really complain.

I'd also note that QF have tried to balance the salt/sugar/stodge aspect of airline food by offering fresh fruit on their longhaul flights. And as noted by NZ_flyer, they hand out the snack bag halfway through the flight, not just before landing.