your agreement with builder must be containing clause that you would be liable to pay Vat it is your obligation to pay MVAT to builder as you bought an under construction flat from builder. As per ruling of Honorable Supreme Court of India, the sale of under construction flat / property is liable to pay VAT.
2)As per rule 58 of the Maharashtra Value Added Tax Rules, 2005
the sales price may be determined after deducting from the
agreement value; the value of land, labour, chargers for planning,
designing, architects fees, hire charges of machinery etc. The tax is
computed on the value arrived as above. The tax computed as
above is reduced after considering the tax paid on the purchases of
building material (i.e. input tax credit). The tax so determined is
required to be finally paid.
3) in mahrashtra state govt has launched composition scheme for builders wherein vat has to be paid at 1 %of contract value of the flat