"It's not X, it's Y" is for when you know your reader will think X, and you want them to understand the difference between the X they are expecting and the Y that is actually the case.
Here are the two "not just" passages in the article:
> Driven by this discrepancy, I built a simple tracking script. It was not a sophisticated piece of software, just a tool designed to observe how "users" actually interacted with the website. I was not just counting clicks; I was watching behavior.
> The bots operating today are disturbingly good. They are not just hitting your site and leaving; they are programmed to mimic engagement, making your marketing ROI calculations dangerously inaccurate. I began to categorize them.
Both of these passages are using the "not just X, but Y" trope in a purposeful, meaningful way, anticipating what a typical audience member might assume and signaling for them to adjust their expectation. Not just trying to maximize the usage of the trope with random non-sequitur values of X and Y, as GPT does.
(Oh dear, I just said it too.)
It would be interesting to assemble a corpus of meaningful human text with superficial use of AI tropes, put it side-by-side with true AI slop, and see who can tell the difference. I suspect that, in the coming years, this will be a test posed in higher education and job interviews.