If the BR states that authorised signatory can 'do all acts for completing registration formalities' then in my opinion it includes the right to grant a PoA for admitting execution before registrar on behalf of authorised signatory. That itself is an act in furtherance of completing registration formalities
Since the POA does not specifically mention your project but states that grantor is authorised signatory of company required to sign various documents on behalf of company and the BR is also attached to conveyance deed along with this POA, then in my opinion your project is referable in the POA by implication from the BR which is itself attached to conveyance deed
So the BR and POA are not that grave a issues
However there is no harm if a document clarifying the apprehension around the BR and POA, is executed
If company does not accede to your request then you can file a civil suit to compel the company to rectify or clarify the anomalies with regard to the BR and POA.
Alternately since such a suit would take long to resolve (in the event the company contests your suit) and considering the costs involved for the same, you can also ask the company to clarify on the BR and POA on its letterhead duly signed by all the board of directors of company with company seal and stamp affixed
Thereafter you can issue public notice in local newspapers to inform public that the plot is sold to you under a registered conveyance deed and also mention about the company letter giving clarification on BR and POA and thus call for objections from public
Presently you wont face any issues if there is no clarification on the BR and POA but you may face issues when you sell this plot and the buyer has availed bank loan. Its possible that the bank may raise these issues and refuse to sanction loan of buyer and thus your buyer profile may be restricted
Thus as a caution you can go for either rectification or clarification deed and if company does not agree for it then you can opt for public notice route (if company says that it will give clarification on its letter head and not by a separate document) or you can go for a substantive civil suit as these issues may have a bearing on your title in future upon selling
Regardless of the company complying, i suggest that you must adhere to and comply with your contractual obligations under the deed and make balance payment to company under protest and on a without prejudice note