If someone who genuinely wanted to question your expertise and intended to offend you asked "why did you choose this algorithm?" you would be justified in feeling offended. If someone who genuinely wanted to learn and didn't intend to offend you asked the same question your offense would in reality be unjustified.
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.