A larger atom is the same thing as observing it closer: all it's constituents will be (appear) larger, strings, quarks, orbitals, wavelength. It's just a matter of scale. (by larger atom here, I do not mean uranium vs hydrogen, I mean identical but larger).I'm not at all sure an atom having a larger radius means it emits light with a longer wavelength. Even if it did - and there's some evidence the bohr radius was slightly bigger in the passed, I have no idea if it was ever big enough to explain expansion in terms of matter contraction. In fact, an electron would need a higher energy to be at a further distance in a larger atom. while it would emit light it would surely be of shorter wavelegth. this whole idea of matter contraction just doesn't have any relevancy to observed physics.
Just imagine a diagram of an atom emitting a light at some wavelength, then enlarge the whole diagram.
Or just imagine the photon travelling from a far away galaxy, eventually reaching our galaxy which in the meantime has shrunk, making us see a redshifted photon.