Resale of unregistered commercial property

Sir, i have purchased a commercial office from the seller - but this seller has an MOU dated 31 jan 2012 between him and the builder & a sale agreement between him and builder - he has not registered the sale agreement which is dated June 2012.....and has not paid any stamp duty on this... Can I register my current date sale agreement with the seller & pay stamp duty on this & get property transferred in my name ??? The seller is suggesting that we draw a sale agreement keeping the builder as confirming party, and hold back some amount (equivalent to the sram duty with penalty/interest payable by him for not registering the earlier sale agreement on time) & make balance payment to him......... if by 15th April 2016 no stamp duty amnesty scheme is announced, then this amount held back by me can be used for making payment of stamp duty/penalty etc as applicable on his earlier agreement with the builder... can you pls guide if this is correct ??? Is my position secure with this ????