Aerospace controls engineer here - while the airframe might not be passively stable (as is common for civilian aircraft), dynamically unstable aircraft have been stabilized with control software since the 70s [0]. If you've flown on an MD-11, you've flown on an 'aerodynamically flawed' aircraft. Most real systems are dynamically unstable without some kind of controller (implying software) in the loop.
[0] https://en.wikipedia.org/wiki/Relaxed_stability