Also, when you view in Digital Editions, you will see that the next page has a "2" on it.
I think is is some kind of page number?
However, the "1" is actually part of the 4 thumbnails created by the Touch. If you replace the actual thumbnail file with your own, it will not have a "1" on it and it will match your cover file exactly (as long as the proportions are correct).
Because the margins seem to be an effect of the thumbnail creation routine on the Touch I doubt we can do anything simple to the epubs to fix it other than adding a border to the cover. Most covers need some kind of border or margin anyway since they are a different proportion to the Kobo Touch's screen.
Also, remember that the Kobo only creates new thumbnails after a Factory Reset or when the epub is first loaded. Any changes they might make to the firmware would only be evident in new content!