The SFO and Paphos incidents are examples of crew's ignorance of auto flight/ATHRsystem. What they thought should happen was based on the pilots insufficient knowledge of the ATHR and it simply was not designed to happen
I agree partially with that. If the SFO crew had been using manual thrust for the last two months the accident would never have occurred. The auto throttle should be nothing more than one tool that can be used to move the thrust levers, the other method, and it should be the primary go to method, is the pilots hand. We have set up a system whereby that is not the case, the go to method is the automated mode. It may not say that in an FCOM but that is the reality. The brain quickly develops preferred methods of achieving tasks and we have created the situation where the preferred method is the automation and manual manipulation is a bit foreign to us. So ingnorence of the system is a problem, but not as big a problem as re wiring our brains to favour automation over manual handling.
My two cents.