I maybe wrong on this, but I think the Notification Comment only appears in the email notification. The State Change Comment appears in the history of the document.
So if you want something to appear in only the email but not history, use Notification Comment. If you want it in both places, use State Change Comment.
When you perform a state change the State Change Comment area is available to enter comments which will be part of the document history.
If you have not setup notifications on the transition the Notification Comment will be grayed out.
If you have setup notifications the Notification Comment area is available to enter comments which will be part of the notification but not part of the document history.
OK, now I see why there would be two different comments, but what confused me was that both comments show up in the notification. So it seems that the document history shows only the State Change comments, but the notification itself actually shows both the State Change comment _and_ the Notification comment (at least when EPDM notifications are used).
I hadn't checked the document history so all I had seen was the notification, which makes the two comments appear redundant.