on the other hand, i could see someone simply meaning 'why do you use qwerty' as 'what's the history of your using qwerty'. i wonder if this linguistic issue might cause us to conflate facts of the past with motivations.

I tend to say ‘Why do you use QWERTY?’ for the question that Eliezer was writing about, and ‘How come you use QWERTY?’ for the question of history. As far as I know, this isn't justified by any recognised rule of English grammar, but it feels right to me.

You can also use more precise phrasing: ‘Why do you choose to use QWERTY?’, ‘How did it come about that you use QWERTY?’. But who wants to use more words than necessary?