I’d go with “I think X might work better here - is there a reason you didn’t use it?” - because the answer might just be “oh, I didn’t think of that, cool, I’ll do it that way”. Whereas your question implies that they should have thought of it, which could be perceived as an underhanded insult if they didn’t.
> I'm not clever enough to understand why you didn't use sshd. It would take a fucking genius to figure that out.
I think saying "i'm not clever enough" (one of the options presented in the article) was never a realistic option given the premise of the article, which is: "a problem somebody’s been working on for a week or a month or maybe years". In this context it's also the least likely interpretation of any other question unless you are a telepath, the limitations on the time you've spent thinking about it are implicit, it does not mean you are incapable of figuring it out...
The other person has been working on this significantly longer than you, this is the reason you can't quickly deduce everything they know. The whole point of this type of questioning is to try and extract some of the results of work the other person has already achieved, for the purpose of better understanding the problem, guide further enquiry and possibly allow you to make useful suggestions.
> I can't figure out the reason X doesn't work
This is more often what I really mean, i.e there is some obvious solution (to me at least), but it's too obvious that they have likely already considered it and there is an issue with it... but they have been working on the problem longer than me - so tell me. Occasionally the solution is obscure enough or slightly unfamiliar to them that it slipped their mind - in which case it's an "oh of course" moment, which also causes no hurt feelings since you aren't trying to rub it in.