Tom, can I ask what your professional experience within aviation consists of?
You do understand that flight dynamics, when applied to an aircraft, is concerned with the stability, and movement, of a body along three axes due to the changing angle of attack to the airflow.
The influence of the shape of the earth at this level is neglible.
In aviation, we make lots of assumptions to simplify things in order to focus on the important areas being studied at the time. When studying flight dynamics, one might assume the earth is flat. When starting to study radar theory, one might assume all aircraft reflect the same amount of radar energy (spoiler, this isn't true either!). In many cases we assume the air is the International Standard Atmosphere, within which are several other assumptions of air pressure, density, temperature, adiabatic lapse rate etc. This doesn't mean we believe the air pressure across the whole earth at sea level is 15 degrees celsius, nor that the air pressure across the whole earth at sea level is 1013.25hPa.
that pilots are taught to fly over a FE, as demonstrated in that guide from a flight dynamics course.
Are you a pilot? I've never been taught or told that the earth is flat in any of my training to be a pilot, or an air traffic controller, nor have I trained that to any of my trainees over the past 23 years.