IMHO those that say they fully understand the system, actually don't completely.
It doesn't matter. Clearly no one has equal understanding as those who actually developed/designed the logic/system. But you don't need to study one million lines of code to operate them safely. A beauty of those systems however is they are telling you exactly what they are doing at any moment - one glance at the top of the PFD and 777/737/747..etc pilot knows exactly what autopilot/throttle are doing at the moment - if you don't like what they are doing - either force them to do what you want or fly manually. When I transitioned from an old Cessna to a highly sophisticated G1000 equipped aircraft the first thing they force feed you during training is to always check the autopilot status bar - don't assume it is doing something unless you verify what it is actually doing. In other words flipping switches or pressing buttons without verification is simply a very poor airmanship which as no place even among amateur aviators least commercial ones.