First of all remember that the builder will be selling the property in the capacity of the GPA only on behalf of the original owner and the understanding between them in this regard is not your problem.
As far as you are concerned you are buying a new property from a seller who has a marketable title to sell the property.
Hence it is important to scrutinise the title documents as well as the title link documents including the encumbrance certificate, mutation records issued by the land revenue department, building plan, layout approval plan, completion certificate, any other relevant documents. After obtaining copy of all these documents, the most important thing that you should do is to get a legal opinion from a local experienced lawyer before making payment.
Based on the opinion you may proceed with the purchase.