a) Whenever you enable the left-hand fuel pumps, be it first or last, the APU shuts down. Enabling the right and center ones it won’t. Considering the in-game checklist wants them on, that sounds like a grave annoyance.
b) Pulling throttle to zero won’t disengage autothrottle, at least not after a longer flight. Being close to touch down, requiring to fumble with keyboard keycombos or mouse jockeying to force-disable it makes weird of an experience.
When starting from the runway: when I click the continue I can see quickly that the engines turning down rapidly to 1% and the other to 0% after that I get the message to turn the engines on with ctrl + e. When I do that they both go to 1%. Same happens with AI on.
A couple of other odd things to try, probably not going to work, but
did you delete your rolling cache? and if you made a manual cache did you remove it?
Also, recheck your assists, make sure all are turned off.
I’m not sure my issue is the same as OP’s, mine was a total loss of all electrical systems. It didn’t act like a bug necessarily (i.e. the plane was indicating exactly what it was doing, which was nothing) and I was never able to reproduce it, so I’m still not sure if it was really a bug or if I made some sort of brain fart when starting up the plane.