Querrry is not clear. State the situation here not some asumption.
If the buolder is registered under vat & st, he may charge that, but he need to provide you with the TIN & ST numbers on a tax invoice. Do make such payments always vide DD, cheque or bank transfer to the name from which the invoice is raised.
A builder can not transfer the ownership to two different parties. If the sale deed is executed on your name, its your property and builder can not transfer the ownership to any society. However, if a RWA is registered later on, you may opt to be a member to enjoy the services and to contribute in maintaining the locality. But the ownership remains with you only.