You literally transmute matter at will, you do not need to fight Killcannon just turn his robot arm into cheese or something. Your nemesis is a villain that you do not need to consider the whole cannot effect living tissue thing for even a second. That is all.
Even can manipulate atoms, correct?
Everything is made out of atoms.
What if Eve turns all viltrumites into water or something?
Conversely, the inner ear thing can be exploited by making a lower pressure gas be the gas inside the ear behind the membrane, or just turn some of the air in their ear canal into water and then squeeze until their ears pop.
What if she just somehow I dunno create a sonic boom anywhere she wants in the air. She can probably manipulate the pressure waves.