The Evolutionary Argument Against Naturalism (EAAN) is an argument against naturalism not atheism in general nor any specific evolution theory. Evolution viewed theistically includes the add-on that evolution is guided. Evolution viewed naturalistically includes the add-on that evolution is unguided. Plantinga needs to describe naturalism in such a way that when combined with evolution it leads to unreliability of cognitive functions. This requires describing the way belief relates to behavior given naturalism or describing the materialistic view of human beings given naturalism.
According to the Wikipedia article Plantinga reformulated the argument in 2008 that originally appeared in 1993 in Warrant and Proper Function. In 1994 he published a version in “Naturalism Defeated” (ND) that is available online. The current version is in Where the Conflict Really Lies (WTCRL).
Premise 1, or “Darwin’s doubt”, states the following taken from WTCRL, page 316:
P(R|N&E) is low.
'R' is the proposition that our cognitive faculties are reliable. ‘E’ refers to evolution without either the theistic add-on of guided or the naturalist add-on of unguided. 'N' is the proposition that naturalism, as Plantinga will describe it, is true.
What Plantinga needs to clarify is how naturalism explains the content of our cognitive processes using evolution.
In the first version, he describes the relationship between beliefs and behavior. There are four ways of splitting the possibilities given naturalism. Either beliefs have no effect upon behavior or they do have an effect upon behavior. If they have an effect upon behavior those effects may be maladaptive or adaptive. If they do not have an effect it is either because of epiphenomenalism or semantic epiphenomenalism. In this version he is not specific about what causes behavior. Behavior is “caused by something or other--perhaps neural impulses--which would be caused by other organic conditions including sensory stimulation” (ND, 7).
In the second version, he claims “nearly all naturalists are also materialists with respect to human beings; they hold that human beings are material objects” (WTCRL, 318) What he will refer to as “naturalism” will also contain this “materialism”. This allows him to be specific: “a belief will be a neuronal event or structure” (WTCRL, 321). It is by specifying the “something or other” left vague in the previous version as “neurophysiological properties” that allows him to simplify the argument to consider only two cases: reductive and non-reductive materialism.