Anybody who booked or made partial payments for their under construction properties before July 1st, 2017 should not face any increased costs under the new GST scheme. Any builder demanding more money because of GST is in violation of profiteering u/s 171 of GST law (although these are not effective yet).
Previously, builders were not eligible to claim input tax credit (ITC) for excise, VAT and Entry taxes that they paid for construction materials. Therefore, the taxes on construction materials, cement, etc., were passed on to the customer with higher prices for the properties. However, under the new GST scheme builders can avail of ITC, which means the input taxes should no longer be a part of the flat prices. CBEC recently guided builders to not make unreasonable increases in prices due to GST. If there is any overcharging, then the excess tax must be paid to the government, else the builder under anti-profiteering laws will find him/herself in difficulty.