A well designed automated system trades resources or resource efficiency for convenience.

Ballistae are trading efficiency for even more inconvenience.

The trophy thing and the attacking the player thing has a clear balancing reason put behind it: make it unusable on bosses (or until you beat them at least once).

Any sane dev would have just made then unable to target bosses but instead we get a system that goes against the principle of its purpose.

Yes you can work around certain issues and streamline the tedious process, but that doesn't change the fact that it's tedious.
Remember that you also consume ammo to do something that would cost you nothing or almost nothing if you did it yourself...

In the end you're wasting time and resources (which is more time wasted to collect them) on something that is supposed to help you not waste time.

Also they put in an enemy in that is extra tanky when being shot from the front.
The game very clearly doesn't want you to use them so why do they exist?