[natep]

The problem is that you can't fully control the meaning that someone takes from your statement. As a spacecraft enginner that knows many of the possible justifications for these "why don't they just"s, it's the negative connotation that springs to mind first, even without the "just". I think it is because that phrase is often used in the imperative sense, and not in a knowledge-seeking sense. Google autocomplete for "why don't you" suggests "stay", "get a job", "love me", and "do right" and if someone were to ask me any of those questions, I would not assume they were sincerely wondering anything.

Now, if you're wondering how better to phrase your questions of this sort, I'm afraid I don't have any specifics, because I'm not sure if I'm just as guilty of this, or if I've successfully rephrased my questions of this sort. What I do is try to imagine that I've spent years designing, building, and debugging the thing in question, and gone through multiple reviews by outside organizations where every design decision was scrutinized, and had many meetings with coworkers (formal and informal) to discuss the thing in question. And then I ask my question in the affirmative, rather than in the negative, such as:

"Why did you do X, would Y also work?"

"I would have done Y. What is it about X or Y that I am missing?"