Flat approved plan deviation

I have booked a 2bhk flat near Barasat under Kolkata Suburban. This property is not registered under HIRA or RERA .Many banks rejecting my home loan application due to deviation from approved plan of that project. It’s a G+3 building having 3- two bhk flats and 1 - one bhk flat in every floor ( 1st to 3rd) as per the municipality approved plan. But, the builder is making it as 3 - two bhk flats in every floor and also changing the lift orientation. According to builder this are very common issues. For that he will produce completion certificate after 2 years, then it will be okay. By that time, he is forcing me to take home loan from pre-approved LIC HFL. As per flat agreement, i have still one year to pay remaining amount otherwise he will charge me 25% of the amount paid. I have already paid him 40% of the total amount through bank cheque. In the agreement, it is also mentioned that if he fails to deliver the flat within stipulated time he will refund the money with bank interest. Queries: 1. Are these types of properties legal if completion certificate provided? 2. Can I claim the whole amount paid without giving any penalty charges to the builder, as it is not my fault?