The 40 seconds is misleading. The MCAS system could in the worst case run the trim full nose down in 40 seconds (it's active for 10 seconds with a 5 second delay between cycles) if the pilot does nothing to counter it.

It's like if you are driving and the road starts to curve. If you do nothing, yes you will get to a point where a crash is unavoidable. But you know that when your car is not following the road, you turn the steering wheel. Pilots know that when they have to pull the yoke to keep the plane level, they need to trim.

The problem is that if you do the intuitive thing (which is what pilots are trained to do for most trim overruns - pull on the stick to counter the trim), the MCAS goes through the increasing cycle to full nose-down. It's 40 seconds to realize that your usual strategy isn't working, figure out what to actually do, and then turn off the exact right system.