> before navigating away from trusting the big O analysis.

I don't think that's the spirit of the article. The spirit is to not assume O(1) is O(1) if you work with a physical computer and care about anything beyond how many times your program counter increments. Make sure to use big O notation that includes the complexities of carrying out those single instructions.

If you work with more than 32k of data, you either need to modify your big O to take latency into account, or you're assuming some worst case cache level, which is fine, and what you're doing with an idealistic big O...but that's a terrible assumption if you're actually trying to achieve speed or realistic metrics.