I've never understood the "number of the atoms in the universe" argument. The number of states the universe can be in doesn't seem to be equal to the number of atoms. For example, just two atoms could encode lots of numbers simply by using their distance. Quantum physics would affect it, but I mean in principle: we are not switching atoms on and off to encode state.
It's not states, it's logarithmic of states (# of dimensions of finite size) . Think about writing down a number. One atom per digit is a pretty natural heuristic for the optimal spatial cost of information. Yes you can get clever, but there's no point, were already at astronomical levels of imprecision.
Another argument would perhaps be the energy required to do the computation. Maybe that relates more directly to the number of atoms in the universe, via Einstein's equation?