Resolution enhancement for a 2wire PT100 setup with ADC and no external amplification
I'm working on a PT100 based temperature probe sensor to read
  temperature difference between two points inside a pipe with flowing
  water


Consider going for a differential measurement as per the method used in a wheatstone bridge. The ADC you have chosen seems ideal for that: -


  This product line has fully differential analog inputs, making it
  compatible with a wide variety of sensor, industrial control or
  process control applications.




This means you only need one ADC.