As far as i know when you buy a flat you buy two things from the builder 1. Undivided Land of Share and 2. The flat.
Both VAT and Service Tax (As on Jan 2013 ...Service Tax @ 12.36% on 25% of BASIC Price ( if Land Cost is included ) otherwise 12.36% on 33% of Basic Sale price ) need to be paid on basic selling price of the flat and not on Undivided Land of Share.