I did test the Flak turret, and added the overPrediction variable to it yesterday after seeing that it tended to, well, over-predict. After checking the enemy and bullet velocities to be correct, I tested again (today), and it seems that the prediction fudges up most when (1) the enemy is one of the "fast" ones and it's moving at least 45 degrees while the bullet gets there, or (2) the enemy has just gotten in range and the turret fires almost immediately without rotating all the way toward the target. However, even after completely removing "smooth" rotation and/or adding a condition to fire only within 1-2 degrees of the target angle, the inaccuracy persisted, so that can't be the main cause. I ended up removing the overPrediction variable, since in some cases it tended to under-predict as well.
You're right that there shouldn't need to be any tweaking necessary, but at this point, I have no idea what's causing the inaccuracy and it would be easier for me to just buff the mortar turret in some way to compensate for this, instead of spending hours bug-hunting.