You can't. I have the same problem ("being Mr Logic"), and my girlfriend points that out to me a lot. Each time she does, it feels like she's accusing me of actively trying to be that way -- of being broken. She's not, of course. That's just how it feels to Mr Logic.

And maybe people like us are broken, in a sense. It feels like I'm missing something everyone else around me seems to have: an ability to immediately understand the reason why people phrase things the way they do.

The person you're referring to probably knows he has the problem and has forgotten about it. If you want to point it out to him, pretend like you're pointing out an embarrasing bad habit, like picking his nose. So you probably want to tell him in private, etc. Also he'll probably deny having the problem. Let him deny it. Just tell him specific examples of what you've noticed. The more specific, the better. A video would be ideal. (Not that I think you'll get one; I'm just trying to convey that telling him specific examples is very important, because otherwise he won't be able to make the mental leap "I have a problem" => "Here's how I fix it".)