The point is you can only make a judgement based on the context as the article states, intention is often invisible and difficult to communicate. Changing "why" to "how " is one potential way of communicating intention but it's not perfect. People will always make a judgement based on the total sum of the context that conversation might be happening in.
Another variation: "What's your thinking behind choosing this algorithm?" That has worked well for me over the years.
To take the example from your parent, some sort of problem where you had to choose an algorithm to solve some problem. There are multiple choices that have their pros and cons.
Mh, very interesting! Why did you choose that algorithm?
Now the very same one:
Mh, very interesting! Why did you choose that algorithm?
The point after all this being that the word why can very easily be interpreted this way, which is harder to do when using these other words in part also because you have to structure the sentence in a less 'violent' way.
Perhaps even better, albeit informal: "Why this algorithm?"
It’s mostly tactics on how to negotiate well, and one piece of advice I’ve adopted is to start my questions with “what” or “how”, not “why”.
“Why” comes across as interrogative; forcing “what” or “how” creates enough time to reassess the actual uncertainty and rephrase as a curiosity question, not an implicit accusation of wrongheadedness.
“Why did you choose this algorithm” becomes “how did you choose this algorithm?” or “what factors did you consider when choosing this algorithm?”
It can be manipulative when done in isolation. My other main takeaway from the book was to have a genuine interest and concern for the other person’s needs, even when you disagree.
Between the trick and the mindset, I’ve found it’s served me well.