I think it was rejected cause Assalt confused the Beast's black hole for an actual black hole (like he did in the Aku vs Beast Cole thread) which isn't the case here as the Beast's black holes aren't actual black holes, we just call them that for simplicity
We have clips of John's black holes absorbing Cole's pure electricity attacks with his black hole, and we know that it breaks down matter and absorbs it (thats how he rebuilt his body at the beginning of inFamous 2), so if he absorbs and breaks down something like electricity, which is composed of subatomic particles like electrons and leptons, then we know he can control matter at the macro-quantic level, and latter repurpose it to rebuild his body.
We also know that he can absorb Cole's rockets, which are electromagnetically bound kinetic charges. Electromagnetic particles are generally considered elementary particles, which is macro-quantic.
Also, we know that John can manipulate Ray Field radiation, which is confirmed to be an actual radiation by Dr. Wolfe. Since its a real radiation, and can cause cancer like disease, than it must be composed of high speed particles, since those are what cause cancer in the first place (basically they shoot "through" your body and knock a few molecules lose, which is what causes abnormalities in cell growth) which is at the very least a sub atomic feat.
Even Cole, before gaining John's powers, could absorb Ionic Charges, which are ions composed of Ray Field energy, and could manipulate them to enhance his powers.