Does swapping the inputs cause increase in the common mode noise in this scenario?
This answer was given prior to the OP changing the question following the observations I made in my answer directly below.


  Is that correct to say for such circuit setup in Figure2, if we swap
  the inputs common mode noise component will increase. Am I modelling
  the issue and interpreting what happens correct?


In figure 1, the common mode noise is shorted to ground hence there is no common mode noise to interfere with the input. In figure 2, the common mode noise source connects directly to the input. What do you really expect under these circumstances?



EDIT - answer to edited question

Scenario 1 applies somewhat less than 50% of the common-mode noise to the input via a 3.3 uF capacitor. Scenario 2 applies somewhat less than all the common-mode noise to the same input (C2 now grounds some of the CM noise).  If you want to show it correctly on your transient graphs, reduce your differential voltage to zero volts and re-plot.