Combat trim doesn’t take into account the dropping of flaps or gear,it also doesn’t account for missing parts.
Some players like to toggle it on and off as they require and some players even prefer to trim the planes manually,myself it usually just leave it on and on the odd occasion I will toggle it off to stop the nose rise when I’m deploying flaps.
The one advantage CT gives you is it reduces pilot work load and it simply works on a scale,x speed gives you Y setting and is constant ally changing as your speed changes. I have pitch and roll mapped to a 4way,this allows me to use trim to correct for missing wing parts and to pull up out of dives in planes that tend to get stiff at high speeds.
As with most things in game….YMMV.