Well, you have complicated the simple thing which could have been done by a single composite agreement only.
In one composite sae agreement and subsequently sale adeed both the landowner and the developer as confirming could have singed the deed.
Since the sale deed has not been made as yet, you better make the landowner as the Vendor and the developer as confirming party in the Deed of Conveyance. This is how transfer of flat is done whether there is joint development agreement in place.