No Fly, let me answer your questions as best I can.
With respect to understanding the system as well as or almost as well as the software engineers, if anyone that has done a Boeing 777 TR in the last 10 years does have this level of knowledge....I'd be surprised. Put simply, the level of in depth knowledge provided has been significantly reduced, why? I guess because Boeing have decided that EICAS is there to solve and manage any abnormals, similarly the MEL provides relief and operational guidance for all those pesky unservicabilities (including A/throttles etc)
As to how the beast thinks? Well again put simply, I use the automation when required or compelled too and in such a way as to allow me to think for the aeroplane (which is how Boeing designed it to be).
With respect to understanding vs manipulation skill and hand flying, like I said, the aircraft flys just like a big C172....if you can understand those basic fundamentals, you can understand flying the 777.
I have an immense amount of confidence in the overall design philosophy as well as the flight control and system redundancy, it means that on the day when it all goes wrong I know that pitch and power will = performance.