An agreement with the builder is contract between two parties and is governed by the local laws. E.g. In Maharashtra, MOFA clauses will be considered the law if there is anything in the actual agreement which is against MOFA.
However, commercial terms such as late payment etc. is normally decided between parties and the agreement is normally prepared by the builder and is normally one sided benefitting the builder so he may have put a clause that the late payment is calculated from the date of his demand even if the concerned slab or work is not over. So you may have to pay the late payement charges as demanded by him since you may have signed the agreement.
However, you can neogitate with him and in good faith he may also waive or reduce the late payment charges or you can go to court to fight for your right which may be difficult to prove and you will lose time and money and also be unable to get possession of your flat until full money is paid to the builder.
My advice will be to talk to the builder and clear the issues as you are yet to take the possession.
I normall y advice my clients to avoid buying flats underconstruction as builders are known to demand money as per their wishes and you also have to pay VAT on the total agreement value. Since you are going to associate with the buidler for a longer time period you will have to face problems if the builder is crooked which many of the common people think they are.
So please go for ready property in future. The higher price is worth the reduced tension and you can invest your money in plots of land where there is no builder involvement.
S Jadhav