I think I am getting confused with thrust and speed.
Could you, say, pump thrust up to its max then leave the throttle at the mid/ neutral point and the control the ship with up down left etc.
What is the point of the thrust? Is it just another but more powerful jet like the up down left etc?
With flight assist on your throttle position commands a 'Speed' using the main thrusters. With flight assist off your throttle position commands a thrust output using the main thrusters.
Here's an example using my Python at it's current weight -
Flight assist on 25% throttle - The ship will accelerate and maintain a speed of 52 m/s (thrust will vary to achieve that speed)
Flight assist off 25% throttle - The ship will accelerate to 52 m/s and continue slowly accelerating at 25% thrust until it reaches it's maximum speed limit.
FA-OFF you set a specific thrust setting using the throttle, the ship will accelerate accordingly. FA-ON you set a specific speed using the throttle, the computers adjust the appropriate amount of thrust to maintain your requested speed.
Edit - your best bet is to have a search on youtube, much easier to understand when watching it in action.
Cheers