Your image actually visualizes the problem exactly. If the target and shooter are at the same height, the shot is pinpoint accurate.
That image is not taken with orthographic projection and your drawing is made as if it is made on a perfect X / Y plane. I can come up with another angle that would proof the opposite.
The observation of BlackYps is solid and counteracts your observation: if what you say is true, then the projectile should hit the ground in front of an extractor when the extractor is at a higher altitude. It doesn't - it still tries to hit it somewhere behind it.
There is no such thing as a "partial" hit. Either the shot connects or it doesn't.
There is such a thing as a partial hit if your projectiles split up into 4 separate projectiles and two hit the target while the other two don't. You mentioned this behavior in your post.
This is an interesting pattern I hadn't noticed. I wonder if the problem can be worked around by increasing the minimum muzzle velocity of the shot, or by changing the projectile's behavior. (Increase speed OnCreate if target is higher, reduce of target is lower.)
Do you want me to share the small mod I made for testing this? Then you can tweak around