Why are caps configured this way in EMC filters?
So you have 3-phase power. There is noise that is line-to-line and noise that is common mode. The caps across the lines are in the right position to filter the line-to-line noise, and the single cap to ground can filter the common mode noise. If you used your method, the capacitance between phases would be less. 

There may also be a consideration that the X capacitors are cheaper and smaller for the same capacitance (if you can even buy that capacitance) as compared to the Y capacitor (because the requirements for Y caps are so much more stringent), so it makes sense to minimize the number of Y capacitors (it also reduces the likelihood of an unsafe failure by 3:1).