Reason of putting clarified ghee on Modak
Golden goodness of ghee has a special value in the culture and cuisine of Indian sub-continent since ancient times. Ayurveda suggests it promotes digestion and increase the absorption of nutrients. 

Adding warm ghee to any meal enhances the taste significantly. An example is the 'tadka/tarka' added to lentils('daal') or pouring ghee over boiled rice to enhance the taste. Probably the main reason of putting ghee on steamed Modak is to enhance the taste. 

From the story behind the traditional association of Modak with this festival my guess is that ghee was added to Modak to make it soft, tasty, easy to eat and filling.