Sanctioned Amount Vs Disbursed amount, EMI is charged on what?

I am taking a loan for a flat in bangalore. hdfc tells me that the sanctioned amount has to be inclusive of registration charges as per bangalore rules. if the final amount disbursed is less than the sanctioned amount, because I intend to make some payments through my pocket, will i attract any penalty or fine for the same? I am trying to get the bank to reduce the sanctioned amount but the bank refuses to do so, since they have the papers from the builder, and will not come down to a figure we want.