1) The difference between the agreement value and guidance value is obviously the cash component. If cash is paid for the difference, any cash transaction for Rs 2 Lakhs and above attracts penalty u/s 269ST of the Income Tax Act in the hands of the seller. Also there is a risk of Income Tax search if the cash component is significant and the property value is high.
2) The seller will be assessed for capital gains on the sale value as per sale deed and is entitled to indexation, exemptions and concessional rate, if the capital gains are long term. However, the seller will be assessed for the difference amount as other income u/s 56 and will be assessed at normal slab rates.
3) The tax percentage post indexation is 20%+4% of 20% towards Health and Education Cess. Surcharge will be varying from 10% to 15% depending upon the quantum of LTCG.
I suggest that the seller may insist upon registering the actual sale value only to avoid additional tax liability and penalty.