Dark matter is a problem from cosmology and astronomy, that maybe has a solution in an extension to the standard model. Maybe it hasn't and that solution will come from elsewhere, maybe there is a totally cosmological explanation after all. In all cases, the dark matter problem is not a contradiction to the standard model in our current experiments. If there were a particle-physics explanation to dark matter, it would be a sufficiently small alteration to the standard model that our current experiments couldn't tell the difference, to within experimental error. That's how confirmation and new models in physics work.

The standard model is so descriptive and accurate, there is just no room for extensions which predict new physics but are still consistent with existing data.

Also, "modern physics" is a term of art, vs "classical physics".

That then contradicts the fact that ions form orbitals according to their number of electrons, not according to their nuclear properties. That was also known before quantum mechanics.