Two of my brothers-in-law (And their wives) had houses built with "safe rooms" included in the basement walls. Both are outside the footprint of the house (one under the front porch and one just off the front porch). Both could be easily secured with a vault door. Both would require digging down from the top in the event of a house collapse.
Getting these things in your house aren't really a big deal.
As far as tax purposes, I have no idea how that works. I'm sure it works differently for different states, counties, townships, etc.
Once the walls have been poured...you can piece-meal it together over a few years and not incur any tax hits until if/when it's finished.