Evolutionary psychology holds that the human mind is not a

Basically, in this sentence, the parallel structure is not actually "not X but Y"; it's just "X but Y".

background:
structure 1: "not X but Y"
this construction signifies that "X" is expected, normal, or customary in the given situation but that "Y" is what is actually present / has happened / will happen.
for instance:
Restaurant X's "hamburgers" are made not of actual hamburger but of turkey.

structure 2: "X but Y"
this construction signifies some sort of general contrast between X and Y, but lacks the semantic sense that Y is a substitute for X.
for instance:
i am not a doctor but can fix your broken finger.

so, the correct answer to this problem can be understood as a case of structure #2 -- note my example above ("i am not a doctor but can fix your broken finger"), which will also appear incorrect if you try to process it as structure #1.

A: The human mind is not a "blank slate," but instead that it comprises specialized mental mechanisms.
Here, the portions in bold -- is a blank slate (verb + noun phrase) and that it comprises specialized mental mechanisms (that-clause) -- are not parallel forms.
Eliminate A.

OA : The human mind is not a "blank slate" but instead comprises specialized mental mechanisms.
Here, the portions in bold -- is a blank slate (verb + noun phrase) and comprises specialized mental mechanisms (verb + noun phrase) are parallel forms.
In accordance with the rule above, not correctly follows the linking verb is.

(C) The human mind, instead of a "blank slate," it ( human mind) comprises specialized mental mechanisms that have been developed to solve - have been - something that started in past and still continues , where as the original meaning was that these mechanisms were developed . 2nd - but is missing.3rd - it - ambiguous .

D: "rather than it, the human mind comprises" (we can omit "being a 'blank slate'" because it is only a modifier of "it") -- no parallelism whatsoever. "Rather than"-structure required some sort of parallelism:
Rather that Mary, Peter should go.
I bought cheese rather than rice.
With verbs situation is more complicated, but we shouldn't worry about it, because "it" (a word after "rather than") is a pronoun and plays the role of a noun. Here "it" is parallel to "the human mind", but at the same time "it" logically stands for "the human mind", so they are the same thing! (Mary and Peter are different people, and cheese and rice are different products in my examples above)
The second problem with D is that "the human mind" comes after its pronoun "it".
GMAT doesn't like "being" if it's used as a participle.

E: "that rather than the human's mind being X" -- this relative cause is incomplete. "Being" here is a gerund, so it plays the role of a noun. We get: rather than [being]. So what? The thought is completed, of course, in the second that-clause, but it is a mistake. We should complete our "rather than"-thought where we started it (in the first that-clause).
The second mistake is awkwardness. "Something's/somebody's being/doing" provides a hint that the answer is incorrect.

Hence B is the correct answer.