The question limit is one of the rate limits that is imposed to prevent spam. If we would allow a low-reputation (new) user to instantly ask a second question, and a third, and ... the site would be loaded with spam.
The time set is just an arbitrary number. It could have been an hour, or 30 minutes, etc. That 40 minutes should be imposed network-wide, so not sure why one site would show something else.
And as rene commented:
Also it is believed that it takes time to research and ask a good question. 40 minutes seems a reasonable time to allow for that research to happen, which can include, but is not limited to, looking for duplicates on the site you ask your question.
Which seems another good reason it is 40 minutes. Taking some time to do some research yourself is a good idea, you might learn from it too. If you have collected a list of questions to ask, you have to wait unfortunately, or gain enough reputation (125) to bypass the rate-limit.
The full guide on rate limits can be found here: The Complete Rate-Limiting Guide.