Adding on to the answer given above, In "1) You will discover that what you have taken for granted is not natural at all", Not at all speaks about the intensity of the thing being natural. In this case, it means that there is nothing natural about it. In " 2) You will discover that what you have taken for granted is never natural", Never speaks about the number of times you may find it natural. In this case, it means that in no instance would you find what you have taken for granted being natural. It does not speak about the intensity.

"You will discover that what you have taken for granted is not natural at all" In this, "not at all"is an adverb of degree "You will discover that what you have taken for granted is never natural" In this, "never" is an adverb of frequency. These two can be used interchangeably ( 'not at all' can function as an adverb of degree as well as frequency ) in some other examples. However, in this context, the intended meaning is slightly altered when you replace one adverb with the other.