Yes, 4D would be a totally different kind of physical existence. That's what I'm seeing from even trying to compare 2D. Again, my original point, that we cannot even imagine the infinitessimally “thin” 1D view of 2D (like seeing ahead, while being totally unconscious of left and right). It would be a totally different kind of existence.
For 4D, you would need a 3D “retina” that a volume of an image would be projected onto.
As for atoms and orbits, a 4D universe would not be using the Standard Model anyway. So whatever physics it would run on, so much else would be different anyway.
(Just in case; when I mentioned time, I wasn't confusing Minkowski spacetime with Euclidean space; I was just pointing out that in a 4D Euclidean vision, the events of time could be laid out in the new space dimension, so that you could see different times simultaneously. Just a sort of fantasy idea for the “afterlife”. I'm thinking more of places than people. And then; I imagine the 3D portion of this hyperexistence would look different, if your 3D retina would have no way to block out the extra dimension to see one 3D “slice” of time at a time).