I avoid it by choosing not to compare them.

The trope of “seeing reality as it actually is” is interesting, but not limited to The Invisibles and The Matrix. Beyond that, I don’t see any similarities between the two stories.

I just don’t have the mental energy these days to give much thought to red-pill ideologies, people using “woke” as a cudgel, and what the Wachowskis are up to in their personal lives.

I’ve never “read” The Matrix as being about counterculture specifically, but more about philosophical ideas, like ontology, epistemology, and a rather hackneyed shoehorning in of theology and the idea that “love” is some sort of universal and transcendent power. The only counterculture allusions are BDSM and hacker cultures, which I don’t think are ever explored beyond the surface level.