Why apart from when building atoms in the first place, the 3d is the lower energy orbital?
In P element, the energy of 3d is lower than 4s. Look at the link provided below. Only in K and Ca, 4s has lower energy than 3d. 

http://www.cdeep.iitb.ac.in/nptel/Core%20Science/Engineering%20Chemistry%201/Slide/lect6/6_6.htm

Another reason could be because the symmetry of hybridized orbital with d orbital will be more preferred in bonding with that of s orbital, and the molecule obtain more energy compensation with sp3d over sp3s.