the OA in Gmat800 is A : here is the explanation of the GMAT800
B and C are wrong because of the use of whose : whose can refer to canyon or layers.
D is wordy : seen is better than been able to see.
E is wrong because of the use of "making" : the subject og making is unclear : it can refer to the layers or to canyon.
In my view, A is unclear because "with can refer either to canyon or layers
practising these questions.

The sentence should read:
Those who have visited the gaping Grand Canyon have typically seen layers of sediment of different colors that mark the passage of time like the rings in a tree trunk.

Having said this, I guess A comes closest to being the right thing. Though D is also fine, it is too verbose.

E has a problem with "marking"
think with D, the use of typically before been able to makes all the difference...

so in D typically applies to been able to ... whereas it should apply to seen
It's a lousy sentence, but I don't see anything technically wrong with A. Choices B, C, and E are obviously wrong. Choice D, while it appears to be grammatically correct, subtly changes the meaning ("having seen" is not the same as "having been able to see"). So, I would say A is the best of the available choices.
NOTE: Apparently, this question is from Kaplan 800. It's not GMAT quality--not even close. So, I suggest that we NOT expend any more time or energy trying to figure it out.