I'm neither a pilot nor an aerospace engineer, but just from my own sense of logic ...
If I was a pilot, I'd want control of as much as possible. With a little imagination I'm sure you could come up with a scenario where it would be a good thing to turn off or take some other action with any system. Any system could be malfunctioning and causing trouble. If an airplane is in trouble, they met well be over the ocean thousands of miles from the nearest land. The pilot wants to have the means to deal with anything that might happen.
Maybe it's true that 99% of the time there would be no reason to mess with X. But what about that other 1%? To say, "300 people were killed because there was nothing the pilot could do to correct the problem, because the engineers figured that, hey, MOST of the time there would be no reason for the pilot to mess with this", yeah, that would be a problem.
Not on the same scale, but ... Just yesterday I had a problem with a default setting in Microsoft Word. Fortunately for me I was able to change the setting, but I really had to search for it. Maybe it's true that 99% of the time, the default setting is fine and there's no reason to mess with it. But my case was the odd 1%.