Bad news. I checked some of the serial backups of my kobo going back to firmware 1.9.5 and I have NO covers that do not have at least a slight margin on the right edge. Most have margins on the left, right and top. Only the Kepubs have full covers and I am sure they are downloaded separately to the Kepub files since when those books are downloaded and installed as Adobe DRM files you get a different, more generic cover!
I also found out that previous to firmware version 1.9.5, the kepub covers were in color. After 1.9.6, they are also in B/W like side loaded book covers.
I think that currently the best you can do is to add a small white border to the cover to mask the slight (in some cases) margin that is added.
I will try and experiment with different cover settings and will get back with the best cover to border settings I find.
You can always go the hard route and replace the 355x530 file with your cover directly on the Kobo. That works as I am using a custom file for the book I am currently reading. However, this is a pain to do every time.
All the thumbnails I have looked at have that small "1" in the corner?