I would be really surprised if there wasn't more to this than is being reported. In hundreds of security checks ranging from benign to utterly insane and moronic, I've seen rolling eyes, muttering under the breath, and irritated looks but have NEVER seen a stubborn refusal by QF pilots to 'play the game'. If it came down to a choice of believing that both pilots were being completely ridiculous and obnoxious, or Manila airport security staff were being completely ridiculous and obnoxious, well.........
There's no doubt however that in the current climate QF management will want to put a certain spin on this.