From what DNSB said I would hold fire on doing anything. It's only since fw 2.5 was released (last week?) that thumbnails for SD card books were saved at all. Prior to that the Kobo regenerated them every time they were required - always with aspect ratio retained. As there hasn't been a calibre release since fw2.5 was available we don't know what davidfor has already managed to do with the calibre device driver. I'd see what happens with the next calibre release, hopefully Friday.
...It won't make the screensaver banner go away, though.