Since the Flat you intend to buy is in an under construction project and the handing over of possession is yet to be done, the builder can charge a transfer fee provided there is a clause in the sale deed that even after registration but before hand over of the possession of the flat if the registered owner were to sell his right, title and interest in favour of a third party then in such a event also the seller would need to pay the builder a transfer fee for such a transaction.
Only if this is provided for in the sale deed would the builder be justified in demanding this fee. If not, the builder cannot demand this amount, neither are you inclined to pay this.
However since possession has not been given yet, you would need to take an NOC from the builder as the same would be required by you post registration in order to take physical possession of the flat. And in order to get the NOC if the builder demands a fee in the guise of "Transfer Fees" he would be justified in doing so. However the sum of Rs.1,000/- per SFT would be wholly unreasonable.
Each time there is a sale, Stamp duty and registration has to be borne by the Purchaser. There would not be any exemption from this.