Why does sulfate have this structure?
Ultimately those structures are wrong.  Most of the community of chemistry educators teaches that formal charge reduction creates hypervalency.  All modern research and models shows this not to be the case.  You can't hybridize a d orbital and even get the proper tetrahedral geometry here.  Reducing formal charges to 0 makes no real world sense, when sulfur has a measured empirical charge of around 1.7 in sulfate.  

Sulfate is 4 single bonds.  The bond length difference is due to the fact that the sulfur carries extra charge, as does the oxygens.  This ionic like bond is of course going to be shorter than more neutral forms of S-O.  Further, why would two double and two single hybrid bonds average to be the same length as a double bond?  

Essentially any general chemistry solution that invokes d-orbitals as it's solution, outside of transition metal chemistry, is wrong.  Sulfur hexafluoride is not in fact 6 single bonds.  

Unfortunately, biochemists are not going to update their picture of phosphate anytime in the next fifty years because no one cares.  

The fact that basically every science major in the world learns this wrong is abhorrent.