ive seen a few trucks where the flaps on the 2nd gen's, which are very stiff, come down on something and rip the entire fender flare off. so trimming them will help.. they also move in the wind and begin to cut into the paint..
yes you will get rockchips if you take them off..
best bet is to do what you want.. which frying pan is best?
I took my fronts off.. and left my rears on.