Bradley, I think that's a great idea. If the alerter could just be shifted down by about the height of the DSi's top screen, it could be tappable upon appearing (no matter what position the scroll bar is on). That would be very helpful in the way of scrolling.
Another possibility is the addition of a deletion option, as in a clickable 'x' on the alert's upper right-hand corner. Of course, this is for those who don't wish to be bothered at the moment and want to view the message later.