I know calibre sideloads the cover thumbnails that the Kindle uses in Library view, when using Send-to-device. I don't know anything whatsoever about the Kobo

but perhaps there is a similar thumbnail file of some sort for the Kobo, which calibre puts on (and KoboStore would as well) but naturally, sideloaded-over-USB books do not have that done?
Really, this all is what calibre is
for. I would just use calibre to sideload.