There is no need to pay extra 20% for the carpet area change and excavation charges as you are only supposed to pay the charges which were agreed upon when you had booked the flat and you and the builder had executed the builder buyer agreement.
You can file a complaint against the builder in consumer court for deficiency of services and unfair trade practices adopted by him and can claim possession/refund, alongwith interest for delay in giving possession, compensation and litigation expenses.
Alternatively, you can also approach RERA and file a similar complaint against him.