This is actually a problem if you have the T16.000 for example.Your controller only sends commands when you move it. Also, I expect the auto SC will override your throttle. But even without it you can hit a key mapped to 75% throttle on your keyboard and it will work so long as you don't move the throttle.
If you throttle by button to 75% and then reduce speed at the hotas, you actually first accelerate, because the slider starts from 100%.
Many a loop of shame was produced by this circumstance.