Matter manipulation is not the same thing as molecule manipulation. All molecules are matter, but not all all matter is molecules.
Being able to manipulate atoms is more powerful than being able to manipulate molecules, and being able to manipulate sub-atomic particles is more powerful than being able to manipulate atoms, in which sub-atomic particles, atoms, and molecules are all matter. And everyone listed as a molecule manipulators are matter manipulators in which they can affect matter on all levels.
With that said, I wouldn't put Molecule Man in that category, despite his name. He fits in the reality warper tier.