The pills originally come from Lewis Carroll, where Alice could change size by taking them. Jefferson Airplane used that metaphor to sing about psychedelics. The Matrix adapted Carroll's pill motif to represent an alteration in one's perceptions of reality. In the broad sense, yes, in the narrower sense, no.
The Wachowskis themselves pulled from gnosticism, eastern religions etc.
Pahlaniuk used the term "snowflake" to refer to people who were brittle and "not beautiful and unique" (his words from memory). He is/was a left wing anarchist.
I think you've experienced a bit of Mandela effect. Alice in wonderland is in fact mentioned as a metaphor in the movie. However, Alice would eat cake and take pleasant tasting potions to change size.
The famous song White Rabbit by Jefferson Airplane uses an extended metaphor based on Alice In Wonderland, and has the lyrics:
> One pill makes you larger
> And one pill makes you small
> And the ones that mother gives you
> Don't do anything at all
> Go ask Alice
> When she's ten feet tall
I've never read the Alice in Wonderland book, but the Disney adaptation of it from the 50s had cake and a drink I recall, and no pills.
I believe that was the point of both what I and GGGP wrote. Pahlaniuk would not be one of "those who love using the term snowflake", in its current context.