LDO Voltage regulator output unexpected Voltage drop
First of all why am I not getting exact 1.2V rated output from the
  regulator given it satisfies the min input voltage and the dropout
  voltage.


The 1.2 volt regulator (LD39015) has a +/- 2% tolerance on its output hence it could be as low as 1.176 volts. Regarding you altering the value of resistor in series with the input to the regulator you are almost certainly dropping enough voltage to take the input terminal into the regulator beyond its low-drop-out-point.

The device has a quiescent current of 18 uA and, with 100 kohm in series with the input terminal, the voltage formed across that resistor is 1.8 volts. Subtract that from 3.3 volts and the voltage at the input to the regulator is 1.5 volts.