The timer starts from when the comment is posted. But if the email is not approved when the scheduled send time arrives, the email is not sent -- instead, it is sent at the earliest opportunity after the comment becomes approved. This is by design so that the email isn't sent to spam comments.
For example, if you have a delay of 1 day. Example 1:
* Comment posted on Monday, automatically approved
* Email is sent on Tuesday
* Comment posted on Monday, not approved
* Comment approved on Wednesday
* Email is sent on Wednesday.