GST is payable on under-construction property@5% but if the flat/unit is complete then there is no GST on same.
Now there are various components in a flat and not just the basic cost of construction. For example if your total cost of apartment is Rs. 1 crore then 80% of it will be basic cost and the rest 20% as other cost like, IFMS, Car parking, LDC, EEC, etc.
These 20% charges are collected by the builder at the time of final offer of possession and these charges attract different slab of GST and not 5%. These charges are usually at 18%.
Now as you said that the builder will receive the GST from bank, that actually is right because you pay the complete cost including GST. So when you get a loan from bank to pay to builder then that loan will include GST part also and not just the net amount payable to builder.
So, if you take a loan of Rs. 80 lakhs, then it will include the GST part also and builder will give the GST out of that amount to Government. So, builder is technically right in saying that he will receive the money from bank but, logically it is you who is paying the GST to builder by availing a loan for purchasing the apartment. Builder will receive the payment in form of loan availed by you and he will segregate the money in his own income and GST at his end, of which you should not even bother.
Also to clarify, once payment is made to builder the total amount paid is converted to EMI which is paid by you. This EMI is composed of principal and interest only. The interest part of EMI is exempt from GST and there is no component of GST included in interest part of EMI.
If again, GST is levied in EMI then, there will be double taxation as well as a huge burden on the end user/purchaser.
Now when you will receive the final demand at the time of offer of possession then there will be more than one slab of GST. There will be few components on which GST will be levied @5% and other components on which 18% GST will be levied.
Live before you leave.