Buying an endorsed flat from a seller.

Registry of endorsement case flat I'm buying a flat from the seller who is still waiting for possession from the builder. Seller got it in 2015 at price 86lakh from the builder and is now selling at price 2.24 cr which is higher than the original builder buyer agreement. Broker is saying that builder will endorse the transfer from seller to me, but the builder will register it only at price 86 lakh and not 2.24 cr. I'm deducting TDS 1% on full price 2.24 cr but looks like the sale deed and registry will be on price 86 lakh. I want to pay registry for the full amount 2.24 cr but the builder is not ready for that. Please help me with following questions. Is this legal? They are saying this is the norm in endorsement cases. What if I sell this property in future? How will my capital gain get calculated - based on price X or Y? Any other risks given the registry is at a lower price than the purchase price. Note: Bank has already sanctioned me a loan of 1.8cr The agreement to sell made is of 2.24 cr. All the seller documents are properly verified. Thanks!