I don't think that sort of question is the one he is talking about. The Eon Timer thing is answerable, just nobody knows enough about it to answer the question. He seems to be talking about Game Freak Logic questions.
For these type of questions, I've always thought of it as give reasonable conjecture. For example, the answer to the question of why Jirachi and Doom Desire are Steel. I keep these type of questions up. I do hide stuff that you can't even give a reasonable answer to, such as "Why is Pikachu a mouse?"