I don't have a Kobo WiFi to test with, so anything I say is based on reading the driver code, discussions here and in the Kobo forum and how the newer devices work. The processing to sideload books doesn't seem to have changed, so hopefully what I say is correct.
I'm a surprised by the difference in the SD card and internal memory behaviour. The Kobo devices can stop adding books to the internal library if they find one that is bad in some way. I would expect that this affected both types of memory. So, if the driver puts a valid book in the correct place, it should be loaded. One thing is the order the books are processed. If you have one that is stopping the processing, any book sideloaded afterwards will not be processed until the bad book is removed.
The covers are generated from the books by the device. It simply renders the first page and stores that in a few different sizes. The only issue I can think of is if you have 2000 or more books. The files system used is FAT32 and because of the length of the file names, the images directory can only handle about 8000 files. The 1.9.x firmware for the Touch had four covers sizes, so it hit this error around the 2000 book mark. This should include the books on SD card, as the covers for both internal and SD card books are stored in one directory on the internal memory.
There was actually a fix put in for the older devices in calibre 0.9.30. This would have prevented you seeing any books that were on the device that calibre hadn't put there. Your clean-up and resend from calibre would have sidestepped this problem if you were using an older version of calibre.
While I can't easily test the changes, I am interested in fixing the driver for the older Kobo devices. If I know what is not working, then I can look at how to fix it or get more information to help. And there is a good chance that it will be copying changes from the Touch driver.
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