After removing the parts and saving the game during the fight, upon reload, the boss is invisible, doesn't move and can't be harmed.
I can provide the save if you want it.
It's also possible that I saved right as I was dealing lethal damage to the boss, but I don't remember.
Bug on final boss
Re: Bug on final boss
After finishing the game a second time, I'm pretty sure that's what actually happened, seeing as there's a delay between the boss dying and the end sequence kicking in.