I think I've made the case above that it's not merely about "being neurotypical", it's also about being steeped in a very specific culture. That peculiar use of "why did you apply" might as well be described as an idiomatic expression, a play on words that happens to be common in that well-defined context. If you aren't familiar with that usage because you are from a different cultural context (or even something as simple as a different "low-class" socio-economic stratum in the same society), you might misunderstand the question in the exact same way - or perhaps you'll grok it but you'll still be bothered by the implied "dishonesty" in it and be inclined to subvert expectations by starting with a straight and to the point answer, and then getting into the actual topic of why you think you were right to apply.