Yes, I was describing a GA IFR flight. You are correct for the airlines they have the route filed for them by their company. I’m not knowledgable about how the airlines work - perhaps there is an airline pilot here who could chime in on the topic.
It would be a great feature if FS2020 could amend a flight plan with a realistic change in real time. Meanwhile I’ll settle on a fix for the wacky trim algorithm.