Is the emission of a photon from an atom a physical change

Yes

When the electron changes levels, it decreases energy and the atom emits photons. The photon is emitted with the electron moving from a higher energy level to a lower energy level. The energy of the photon is the exact energy that is lost by the electron moving to its lower energy level.

Hope this explanation helps you :D

The problem here is that according to aufbau principle before 3d orbital 4s subshell comes.after filling 3p orbital with electrons you have 4 electrons left, you place two in 4s with opposite spin and the other two in 3d in any of its two orbitals of total five orbitals with the same spin.