I can understand that you want to hit the boss only in the face, but like the OP said, hitting the boss in the face is annoying because it's just a time waster. Even flapping around the orbs and fetuses, I only got hit like twice, so it's not difficult to just flap there and wait, it just wastes time. If there was some way to manipulate where the boss shot, even if what the shots were themselves were random, it would be better and even allow players to try and optimize speedruns of the game. Well, kinda.
I was more annoyed that hitting the ceiling in the main flapping part hurt you; it's rather difficult to control yourself when you have to go from a bare minimum hole to the maximum height hole, and I don't think I've ever managed to successfully pull that off once without hitting the ceiling. I attempted this three times. The first attempt died while flapping because I intentionally went below 9 lives for the so-called "Bad Ending" right away. The second attempt I got to the boss but also died because I was trying to keep my lives low for the bad ending, but I couldn't figure out what to do besides kick back the orbs so the fight just dragged on too long. The third one was the successful run where I noticed the face changing states. Maybe if you made the boss flash a bit, it'd be more noticeable that the orb to the face actually did something?