The first phase of the final boss isn't just for show, the shadows are symbolic of the people that she failed. The switches represent her desire to right these failures. The shadows get more aggressive the more Robin picked dialogue options that offended her allies and more passive the more she picked options that placated them as a representation of how heavily she believes she's failed others.
Furthermore, The shadow representing Agent Black is the only one that can be directly attacked and easily avoided until it fades on its own. As Robin is using a stun-gun, her desire to fix that situation involved being able to avoid killing Black by either knocking her out or leaving the area entirely. Alternatively, it could symbolize her realizing that Black was in so much pain and so far gone that there was no way to help her other than delivering a Mercy Kill.
Speaking of the final boss, the pilot of the Starworm also wields a wrench. The last phase of the battle is just a fight between two birds with wrenches!
The main injuries suffered by the second form of the final boss involve it losing an eye, followed by having a hand ripped off. These are roughly the same injuries suffered by Elro over the course of the game.
Further involving the final boss, the theme of the last phase is titled "Castle Doctrine", which is the same name as a particular legal doctrine which states that, in certain circumstances, force up to and including lethal force may be used to repel invaders from one's property with no legal consequence. Consider how The Birdman sees things. As far as he knows, the planet is his fuel depot (or at least he has the right to use it as such), and humans just showed up out of nowhere one day and started using the Ivory in it. From his perspective, he's the one the castle doctrine applies to!
The Ivory shortage might seem like a plot hole, given that Ivory is produced when a Transcendence fails, as the person's body wastes away into it. The logical means to solve the issue is to use Transcendence as a means of burial, but no one even mentions the idea. But when you see how selfish Mother is, it starts to make sense. There would be a chance the corpse would come back to life as an Agent or a Medium, and then try to usurp her with their new powers. She's trying to prevent a Phlebotinum Rebel from being created.
Considering Agent Black's mental state, how much worse could it have gotten if she had lived as long as Fitzroy?
Considering that the Starworm is actually a giant mech piloted by a birdman, what would it do once its pilot got all the ivory it needed?
Likely, the pilot would fly off trying to find another fuel depot while the planet's death is accelerated due to the lack of Ivory. He'd probably prefer a depot that hasn't been colonized by humans.
Royal winds up trapped on the moon with zero oxygen. Regeneration appears take an act of will, which Royal is all out of, having crossed his Despair Event Horizon - and only works on structural wounds, such as being shot or stabbed. Robin no doubt realizes that he let himself die, and only she could have saved him, if it wasn't for that broken sensor.
You know the gun Mina fires at Robin after breaking into Myron's boat, thinking it's a toy? It looks very similar to the gun used on one of the pupils in the Tower, and furthermore, its projectile is the same as the Starworm's Mind Rape beam. Why is this horrifying? It's implied by a note on the boat that he's been using the gun on Pola and Vonn to keep them doing his bidding.