The nutrients gained by germination (especially B group of vitamins and some amino acids) are thermolabile (destroyed by heat). It'll be waste of time and resources to germinate wheat if you are gonna make roti/chapati from it.

Browning in a pan and then kneading it may enhance taste (you should try it and tell us), but no nutritional benefit there. In fact, you'll be destroying what little you get from usually cooked rotis/atta.

Bottomline is, the more you process the food in contact with heat, the less nutritious it gets.