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The 4s orbital empty is actually lower in energy than than the 3d orbital empty, so starting from the d block elements (with a few exceptions) the 4s orbital fills before the 3d orbital; it just has to do with the electron wanting to fill an energy level "closer" to the nucleus of the atom, but 4s is still considered the outermost energy orbital because during ionization, those electrons are the ones lost. Once the 4s is filled (4s^2) and electrons start occupying the 3d orbital (3d^1,2, 3, etc.), the 3d orbital is lower in energy than the 4s because it is not a "complete" orbital. The "base energy levels of the 3d and the 4s are very close to each other so the difference in the energy levels between the 3d and the 4s fluctuate after Z=20. I hope this didn't confuse you more than before.
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