Yes, there is no such options of 2% stamp duty within a year with the government.

There is possibilities that between builder and first owner only agreement to sale deed had happened and with you they will be performing final deed registration.

Better you can ask 7% receipt on your name as paid stamp duty by you i.e. Government receipt. Or you can stick to your 2nd point.

1.  Stamp Duty once paid via a Registered Deed, is non-refundable, in any way.  Avoid falling into any Traps of such kind.

2.  Irrespective of earlier paid Stamp Duty, IF you are executing a new Deed, you are liable for 6% Stamp Duty + Registration Charges.  This is applicable for every NEW Registration of Sale-Deeds.  No Exemptions applicable, whatsoever.

resale of a property within one year of buying it from a developer would result in the state collecting stamp duty only on the profit from the transaction

Yre option 2 will be feasible

This is confirm that stamp duty paid on ATS shall adjust with sale deed but in your case this is 2nd sale.

Builder to seller and seller to you. Either the ATS had executed between you ans builder than broker was right.

If sub registrar ignore the fact than 2% stamp duty only payable. There will be no refund. Better go with 2%stamp duty.

In no case, difference stamp duty will pay to seller. Indirectly it may be evasion of stamp duty and in future if you sell the flat than this may get notice to sub registrar. At time you may ask to pay, so don`t pay anything to seller.

AND ask seller to get POA from builder to authorize him to sell the flat as through ATS ownership dose not trasfer, and actual owner is builder at present.

no need to pay separate cheque to seller for difference in stamp duty 

there are no buyers for any property  at present and you can dictate your terms for purchase of property 

Yes you can pay the same through separate cheque

In case of Bombay Stamp Act where investor goes in agreement with the builder under this sub-clause 5(g-a)(ii) benefits are given to investors who sell their units within a period of one years. In such a case, for the sale by the investor, the amount of stamp duty paid by the investor is set off against the stamp duty payable by the subsequent Purchaser, though the minimum payable by much Purchaser shall be Rs.1 000.

Surprisingly however this benefit is not available to any investor who does not deal with a Developer 

This mean someone purchased newly build property never occupied by any and if same property sold within 3 years to 2nd buyer entitle to benefit of previous Stamp Duty.

1.  The stamp duty and the registration rules pertaining to state governments vary from each other, hence if the document writer is of this opinion, you may better clarify this from another writer and proceed if it is confirmed.

2. In my opinion, if the seller is executing the registered sale deed for the property proposed to be bought by you, then you may have to pay the applicable stamp duty for this purpose, hence better confirm the information told by the broker before proceeding.

You were advised to confirm this situation from another broker or a document writer in the local before deciding about what is to be done on this because a plain reading of the clause or the rules may  not enable you to correctly interpret the law involved in this.

What you have heard may be right becasue the applicable stamp duty on purchase of the property by a buyer afresh, has to be paid.

The seller may be executing the registered sale deed in your favor however the applicable stamp duty and the registration charges are to be borne by the buyer only.

This is my response to you:

1. Since resell is within one year of purchase, the stamp duty will have to be adjusted as per reading of the article 5;

2. It is advisable that you approach the IGR website: http://igrmaharashtra.gov.in or call their toll free number;

3. You will get much better answer regarding the stamp duty payable from an authorized person;

4. You can also personally or through an agent the office of the sub-registrar to ascertain the true value;

5. Once the office does finalise on the same, pay the same via DD;

6. Consult a local lawyer and take steps.

1. As per the information mentioned in the present query, makes it clear that you have already paid part stamp duty and now wish to pay the rest of the duty.
2. As the above mentioned manner to pay the stamp duty is acceptable as per law.
3. You should not need to ask for the refund and then pay the whole as you can very well now pay the rest at the time of registration of the sale deed.