This is working as intended. "Cursor Target Priority" is designed specifically to focus vehicle firepower only when your cursor is hovering directly over a specific enemy entity (biter, worm, spawner). Firing at arbitrary terrain or trying to implement complex "smart" algorithms (like predictive lead aiming or collateral AoE damage tracking) would likely cause a noticeable performance and UPS hit.
If you want to quickly take full manual control (e.g. to bombard the ground with the mortar), you can instantly override the auto-shooter at any time by pressing your Forced Fire / Shoot Selected key (default C) or Next Weapon key (TAB). As long as you are actively firing manually, the auto-targeting yields and will not interfere with your aim.
In general, my current development focus is on refactoring and splitting the large monolithic mod into modular components, so redesigning these targeting mechanics is not planned for now.