Will my "after tax" dollars in my retirement savings be given similar favorable treatment?
You will receive the FCA, and overall you will be spending the same amount for a given basket of goods that you do today. Remember that 20-25% of consumer shelf prices are due to business taxes & costs related to them. Those business taxes are repealed under the NRST.
The reason for refunding NRST on old business inventory is to make sure you don't pay a double tax, NRST plus corporate income/payroll tax carryovers embedded in the price of goods.
Incidentally, in Europe where they have a NRST, prices for comparable products are considerably higher than they are here.