The validity of the demand made by the registrar office depends on the "Effective Date" mentioned in the Government Order (GO).
Generally, stamp duty is payable based on the rates prevailing on the date the document is presented for registration. Since you presented and the office accepted the document on the 23rd, and they likely issued a temporary receipt or P-number based on the old rates, you have a strong "vested right" argument.
A revision issued on the 21st but only circularized to the sub-registrars on the 29th creates a "limbo" period. Courts in India have frequently held that the public cannot be penalized for a "communication gap" between government departments.
If you choose to contest this, then you invoke Section 47 of the Registration Act, 1908. This section states that a registered document shall operate from the time it would have commenced to operate if no registration had been required (usually the date of execution), not from the time of its registration.
If the online system or the physical counter at Villianur accepted your payment and processed the signature on the 23rd, the transaction was "complete" from your end. The department cannot unilaterally demand more money after the fact unless they can prove the document was "undervalued" at the time of its presentation.
Submit a letter in writing to the District registrar with a copy to the concerned sub-registrar explaining the issue in detail. Mention that the Registration Department's own internal circular (dated [deleted]) was issued after your registration, and thus should not apply to transactions already completed.
You can demand that the document be released under a "provisional" basis or contest the valuation before the Collector.
Since the document was already registered (you mentioned it was processed), check if it has been assigned a regular Doc No. If it has, the Sub-Registrar is legally obligated to return it. If they withhold it, you can approach the Inspector General of Registration (IGR), Puducherry, at the Saram Revenue Complex.