That story is misleading. First, NASA failed the code in 2011 as poorly tested and with little exception handling. The most important part of the design. The fix was to hire more NASA folks who- know how to do systems engineering. The software lead at the time, who came from gaming, blogged about it.
On the hardware. It's modesty legacy Russian and NASA designs. Which means most of the proper systems engineering had been done over the past few decades which the rocket lead for SpaceX, who came from RW, used.
There was ZERO little significant new design here done in pure bottoms up Agile.