The design goal for the software was to make it fly like other 737s. The software did not actually do that, but did "something" that inspectors allowed was just enough different from without to certify. And, in case of equipment failure, or various other circumstances, the software failed completely, because it was just really badly designed. If you knew about the system, you could turn it off in case of trouble, and then the plane would fly fine, just not enough like a real 737 that you could completely ignore the difference.
Then they made it hard to know that the system was there. People who knew how to turn it off could prevent disaster.