This is my response to you:
1. It is not a problem;
2. The document can be signed by GPA holder as well, but then again the GPA has to be registered;
3. If you can come to India for one day and execute and register the tri-party agreement then it will be better;
4. Also the buyer will have to pay the whole consideration to you then only go for registration;
5. Tell the buyer to make a DD of the whole amount;
6. As long the tri-party agreement is registered with the sub-registrar there will be no problem;
7. If the buyer is ok with the builder keeping the document then the you have nothing to worry;
8. Also execute an indemnity bond from the builder stating that if in case the buyer files a case the builder will indemnify you for your loss.